/JOurnal of
`MOLECULAR
`BIOLOGY
`
`EDITOR-IN-CHIEF: J. C. KENDREW
`
`Volume 112, Number 3, 25 May 1977
`
`ACADEMIC PRESS
`London
`New York
`San Francisco
`A Subsidiary of Harcourt Brace Jovanovich, Publishers
`
`JMOBAK 112 (3) 359-542 (1977)
`ISSN No. 0022-2836
`
`PFIZER EX. 1080
`Page 1
`
`

`

`JOURNAL OF MOLECULAR BIOLOGY
`EDITOR-IN -OHIEJI'
`J. C. KENDREW, 7 All Saints Passage, Cambridge CB2 3LS, England.
`A.SSISTA.NT EDITOR
`S. BRENNER, M.R.C. Laboratory of Molecular Biology, University Postgraduate
`Medical School, Hills Road, Cambridge CB2 2QH. England.
`EDITORIAL BOARD
`R. L. BALDWIN, Department of Biochemistry, Stanford University Medical Center,
`Stanford, Calif. 94305, U.S.A.
`M. S. BRETSOHER, M.R.C. Laboratory of Molecular Biology, University Postgraduate
`Medical School, Hills Road, Cambridge CB2 2QH, England.
`C. R. CANTOR, Department of Chemistry, Havemeyer Hall, Columbia University,
`New York, N.Y. 10027, U.S.A.
`J. DAVIES, Department of Biochemistry, University of Wisconsin, Madison, 420
`Henry-Mall, Madison, Wis. 53706, U.S.A.
`W. F. DoVE, McArdle Laboratory for Cancer Research, University of WISconsin,
`Madison, Wis. 53706, U.S.A.
`G. A. GILBERT, Department of Biochemistry, University of Birmingham, P.O. Box
`363, Birmingham B15 2Tl', England.
`M. GoTTESMAN, Laboratory of Molecular Biology, National Cancer Institute, National
`Institutes of Health, Bethesda, Md. 20014, U.S.A.
`R. HUBER, Max-Planck-Institut fiir Biochemie, 8033 Ma.rtinsried bei Miinchen,
`Germany.
`A. KLua, M.R.C. Laboratory of Molecular Biology, University Postgraduate
`Medical School, Hills Road, Cambridge CB2 2QH, England.
`D. E. KosHLAND, Department of Biochemistry, University of California, Berkeley,
`Calif. 94720, U.S.A.
`S. LoWEY, The Rosenstiel Basic Medical Sciences Research Center, Department of
`Biochemistry, Brandeis University, Waltham, Mass. 02154, U.S.A.
`V. LuzZATI, Centre de Genetique Moleculaire, Centre National de la Recherche
`Scientifique, 91 Gif-sur-Yvette, France
`M. F. MooDY, Department of Biology, Brookhaven National Laboratory, Upton,
`L.I., N.Y. 11973, U.S.A.
`D. NATHANS, Department of Microbiology, The Johns Hopkins University School of
`Medicine, 725 N. Wolfe Street, Baltimore, Md. 21205, U.S.A.
`C. C. RIOHARDSON, Department of Biological Chemistry, Harvard Medical School,
`Boston, Mass. 02115, U.S.A.
`P.M. B. WALKER, Department of Zoology, University of Edinburgh, West Mains
`Road, Edinburgh EH9 3JT, Scotland.
`J. C. WANG, Department of Chemistry, University of California., Berkeley, Calif.
`94720, U.S.A.
`K. WEBER, Abteilung Biochemie 1, Max-Plank-Institut fiir Biophysikalische Chemie,
`Postfaoh 968, D3400 Gottingen, W. Germany.
`S. M. WEISsMAN, Department of Human Genetics, School of Medicine, Yale
`University, New Haven, Conn. 06520, U.S.A.
`Published three times a month on the 6th, 16th and 25th at 24-28 Oval Road, London NWl 7DX,
`England by Academic Preas Inc. (London) Limited.
`1977: Volumes 109-117, 36 Issues. Inland, £199.36 including postage and packing; abroad, £239.,0
`including postage and packing.
`Index and Cumulative Contents of Volumes 1 to 20, 21 to 40,41 to 60: inland, £4.00 each; abroad,
`£4.75 each.
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`Air freight and mailing in the U.S.A. by Publications Expediting Inc., 200 Meacham Avenue,
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`
`Copyright© 1977, by Academic Press Inc. (London) Limited.
`
`PFIZER EX. 1080
`Page 2
`
`

`

`J. Mol. Biol. (1977) ll2, 535-542
`
`The Protein Data Bank: A Computer-based Archival File for
`Macromolecular Structures
`
`The Protein Data Bank is a computer-based archival file for macromolecular
`structures. The Bank stores in a uniform format atomic co-ordinates and partial
`bond connectivities, as derived from crystallographic studies. Text included in
`each data entry gives pertinent information for the structure at hand (e.g.
`species from which the molecule has been obtained, resolution of diffraction
`data, literature citations and specifications of secondary structure). In addition
`to atomic co-ordinates and connectivities, the Protein Data Bank stores structure
`factors and phases, although these latter data are not placed in any uniform for(cid:173)
`mat. Input of data to the Bank and general maintenance functions are carried
`out at Brookhaven National Laboratory. All data stored in the Bank are available
`on magnetic tape for public distribution, from Brookhaven (to laboratories in
`the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide) . A
`master file is maintained at Brookhaven and duplicate copies are stored in
`Cambridge and Tokyo. In the future, it is hoped to expand the scope of the
`Protein Data Bank to make available co-ordinates for standard structural
`types (e.g. ex-helix, RNA double-stranded h elix) and representative computer
`programs of utility in the study and interpretation of macromolecular structures.
`
`The Protein Data Bankt (1971 ,1973) was established in 1971 as a computer-based
`archival file for macromolecular structures. The purpose of the Bank is to collect,
`standardize, and distribute atomic co-ordinates and other data from crystallographic
`studies. As the number of solved protein and nucleic acid structures has grown to
`the point where some 107 characters are necessary to represent the co-ordinate
`information currently held, the need for such a computer-readable file has become
`very clear, and demands for the Bank's services have increased accordingly. The
`Protein Data Bank is one of several data base activities in the field of crystallography,
`e.g. the Bibliographic (Kennard et al., 1972) and Structural (Allen et al. , 1973)
`Data Files for organic and organometallic compounds, the Atlas of Macromolecular
`Structure on Microfiche (AMSOM) (Feldmann, 1977), the Bond Index to the Deter(cid:173)
`mination oflnorganic Crystal Structures (BIDICS)t and the Powder Diffraction File.§
`
`(a) Scope
`The Protein Data Bank covers atomic co-ordinates, structure factors and phases
`from diffraction studies of macromolecules. Since most of this information is not
`generally published in the primary literature, the Bank depends for comprehensive(cid:173)
`ness on data supplied directly by the investigators. It is essentially a depository of
`data, held in computer-readable form , in contrast to other data banks that are based
`
`t Protein Data Bank is a misnomer of historical origin, since the file now contains entries for a
`nucleic acid.
`t I. D . Brown, Bond Index to the Determination of Inorganic Crystal Structures, McMaster
`University, Hamilton, Ontario, Canada, LSS 4Ml.
`§American Society for Testing Materials, 1916 Race St., Philadelphia, PA. 19103, U.S A.
`
`535
`
`PFIZER EX. 1080
`Page 3
`
`

`

`536
`
`F. C. BERNSTEIN ET AL.
`TABLE 1
`PTOtein data bank holdings
`
`!DENT
`CODE
`
`tDLECULE
`
`DEPOSITOR
`
`STATUS
`CODE
`
`IADK
`IADH
`ZADH
`ZCHA
`3CHA
`IF AB
`IRE!
`I CPV
`2CPV
`3CPV
`I CAB
`I CAC
`! CPA
`I CHG
`2CNA
`3CHA
`I B5C
`I CYT
`2CYT
`I CYC
`I C2C
`155C
`I EST
`I FDX
`IF XH
`I GCH
`IGPD
`2MHB
`I DHB
`I HHB
`IFDH
`ILHB
`I YHX
`IHIP
`2LDH
`31..DH
`IL YZ
`2L YZ
`3L YZ
`4L YZ
`5L YZ
`6L YZ
`IMDH
`I MBN
`2t13N
`3MBtl
`3P TI
`BPAP
`?.PAP
`3PAP
`4PAP
`5PAP
`6PAP
`7PAP
`I PGK
`2PGK
`IPAB
`IRHS
`2RXN
`I SI·IS
`15GB
`ISBT
`2SBT
`! SO D
`I TLH
`2TLN
`ISRX
`ITHA
`2THA
`3THA
`ITIM
`IPTN
`2PTB
`IPTC
`
`G. SCHULZ
`ADEHYUlTE K INASE
`C.-I. BRANDEN
`ALCOHOL DEHYDROGENASE <ADP-R!Bl
`C. -I. BRAiiDEH
`ALCOHOL DEHYDROGENASE
`(ORTHOPHEHl
`D. BLOW
`ALPHA-CHYMOTRYPS IN <TOSYll
`A. TULIHSKY
`ALPHA-CHYMOTRYPS IN
`R. POLJAK
`ANTIGEN BINDING FRAGMENT <HEW>
`0. EPP. R. HUBER
`BENCE-JONES
`I MMUHOGLOBUL IH REI
`R. KRE TSIHGER
`CALC IUM-B I HD IHG PARVALBUM IH SET 6A
`R . KRETS INGER
`CALC IUM- B IHD I HG PARVALBUMIH SET 6H
`R. KRETSIHGER
`CALCIUM-B IHD IHG PARVALBUMIH SET 61
`K. KAIIHAH
`CAR BOlli C ANHYDRASE B
`K . KAHHAN
`CARBON I C ANHYDRASE C
`W. LI PSCOMB
`CARBOXYP EPTIDASE A
`J. KRAUT
`CH'I'tiOTRYPS I NOGEH
`G. REEKE. G. EDEl MAN
`CONCANAVALIN A
`K . HARDMAN
`CmiCANAVALI N A
`F. 5. t~THEWS
`CYTOCHROI"E B5
`R. DICKERSON
`CYTOCHROME C <ALBACORE, OXIDIZED>
`R. DICKERSON
`CYTOCHROME C <ALBACORE. REDUCED>
`M. KAKUDO
`CYTOCHROME C <BONI TO. HEARTl
`J. KRAU T
`CYTOCHROME C2
`R . TI MKOVICH
`CYTOCHROtE C556
`H. ~TSON
`ELASTASE
`L. JENSEN
`FERREDOX IN
`M. LUDWIG
`FLAVODOX IN (CLOSTRIDIUM MPl
`COHEN. DAVIES . SILVERTON
`GAtV'lH -C HYMOTRYPS IN
`GL YC ERALDEHYDE-3-P-DEHYDROGENASECLOBSTRlM. ROSSMANN
`HEhJGLOBIIi <HORSE. AQUO MET>
`LADNER. HEIDNER. PERUTZ
`HEhJGLOB IIi <HORSE . DEOXY>
`M. PERUTZ. G. FERMI
`HEhJGLOB IIi CHU1·1AIL DEOXYl
`M. PERUTZ. G. FERMI
`HEI"llGLOB IN ( HUMAN. FETAL DEOXYl
`J. FR IER
`HEtklGL OB IN <L Aif'REY>
`W. HENDR I CKSON
`HEXOK INASE (YEAST> Bill
`T. STEITZ
`HIGH POTEI ITI AL
`I RON PRO TEIN
`J . KRAUT
`LACTATE DEH YDROGHIASE
`M. ROS SMANN
`LACTATE DEHYDROGHIASE/NAD/ PYRUVATE
`M. ROSSMANN
`L YSOZYIIE <HE tl EGG-UiiTE . SET W2l
`R. DIAMOND
`L YSOZYI"E CHEN EGG-Ui ITE. SET RS5Dl
`R . D l AMOND
`L YS OZYME <HEN EGG-WHITE . SET RS6Al
`R. DIAtD ND
`L YSOZYI"E CHEN EGG-WHITE. SET RS9Al
`R. D IAI·IOND
`L YSOZYI1E CHEN EGG-Ui!TE. SET RSI2A l
`R . DIAMOND
`LYSOZ'!'tE CHEii EGG-1.1-UTE. SET RS16 l
`R. DIAMOND
`MAL ATE DEH YDROGENASE
`L . BANASZAK
`MYOGLOB IIi CSPERtl WHALE>
`H. ~TS ON
`tiYOGL OI3 I tl (SPE RM UiALE. METl
`T. TAKANO
`MYOGL OB IIi (SPERM !..HALE , DEOXYl
`T. TAKANO
`PA NCPEA TIC TRYPS IN
`INHIBITOR
`R . HUBER
`PAPA IN. II AT I VE
`J. DRENTH
`PAPAIN
`C A C E - I~ L A -AL A -PHE-ALA. CYS- 25l
`J. DRHITH
`PAPIHN CCYS DE R IV OF CYS -25>
`J. DRENTH
`PAPA III <OX IDI ZED CYS - 25>
`J. DREIHH
`PAPA IN CTOS-L YS . CYS - 25>
`J. DRENTH
`PAPA ttl CBZOXY- GL Y-PHE - GL Y. CYS-25)
`J . DREIITH
`J. DREIITH
`PAPA IN CBZOXY- PHE -ALA.CYS-25)
`PHOSPHOGL YC ERATE K IHAS E <YEAST>
`H. ~ TS OI·I
`PHOSPIIOGL YCE RATE K HIASE CHORSEl
`P. EVAHS. D. PHILLIPS
`PREALBUMIH <HUMAN. PLASMAl
`S . OATLEY. D. PHILLIPS
`RIBONUCLEASE S
`H. WYCKOFF
`RUBREDOX IN
`L. JEHSEH
`STAPHYLOCOCCAL NUCLEASE
`F. A. COTTON. E. HAZEH
`STREPTOMYCES GRISEUS PROTEIHASE B
`M. JAMES
`SUBTILISIN BPH'
`J . KRAUT
`J. DREHTH
`SUBTILISIN NOVO
`J. AND D. RICHARDSON
`SUPEROX IDE DISttJTASE
`TI1ERI"()L YS IN <UNREFINED>
`B. MATTHEWS
`THERI"()L YS IN <REF IHEDl
`B. MATTHEWS
`TIHOREDOXIH
`B.-0. SODERBERG
`TRANSF ER RNA <YEAST. PHE>
`J. SUSSMAN. S.-H. KIM
`TRANSFER RNA <YEAST. PHEl
`M. SUNDARALINGAM
`TRAiiSFER RNA <YEAST. PHEl
`JACK. LADNER. KLUG
`TRIOSE PHOSPHATE
`ISOMERASE
`I. WILSON. D . PHILLIPS
`TRYPS IN OiATIVE. PHBl
`FEHLHAI't"ER.BODE.SCH~GER
`FEHLHA~"ER.BODE.SCH~GER
`TRYPS IH<BENZAMIDINE INHIBITED. PH7l
`TRYPS IH/ TRYPSHI
`INHIBITOR Cot·f'LEX
`BODE ET AL.
`
`A
`
`R
`
`~
`R
`
`P
`N
`RP
`
`B
`
`PD
`PD
`P
`P
`P
`P
`P
`P
`A
`
`R
`R
`
`A
`B
`
`UD
`
`A
`
`A
`
`A
`ll
`P
`P
`
`tl
`RH
`N
`
`STATUS CODES
`
`BLANK
`A
`B
`D
`N
`p
`R
`
`STANDARD ENTRY AVAILABLE FOR DISTRIBUTION
`ALPHA CARBON ATOMS OHLY
`BACKBONE ONLY
`NEW DATA HAS BEEN PROMISED
`NEW EIITRY WITH DEPOS !TOR FOR APPROVAL
`IN PREPARATION
`REPLACES AN OUT OF DATE PARAMETER SET
`
`PFIZER EX. 1080
`Page 4
`
`

`

`LETTERS TO THE EDITOR
`
`537
`
`on data ab tracted from cientific publications. The Bank contain · 77 atomic co(cid:173)
`ordinate entries for 4 7 macromolecules (Table 1), t and 13 et of structure factors and
`pha e . The atomic co-ordinate entrie , which include descriptive t ext and partial
`bond connectivities, conform to a uniform format ( ee below), but the structure
`factors and phases are stored in the format received from depositor . All co-ordinate
`entrie are referred to depo itors for verification, before being made available publicly
`through the Bartle
`
`(b) R ecord structure of atomic co-ordinate entries
`Atomic co-ordinate entries consist of records each of 80 characters.t Using the
`punched card analogy, columns 1 to 6 contain a record type identifier, and columns
`7 to 70 contain data.§ Columns 71 to 80 are normally blank, but may contain sequence
`information which i added by the library-file management program UPDATE~
`used to maintain the file on th e Brookhaven CDC CYBER 70/76 computing ystem.
`In order to facilitate retrieval of data from the file, th e first four characters of each
`record define the unique record type, and the syntax of each record i independent of
`the order of records within a ny entry for a pa rticular macromolecule. (In the ma ter
`file, thi order is always fixed .) Atomic co-ordinate data contributed by depo itors
`are processed into the st andard format with program MACMOL, II which a! o subj ects
`the data to certain nomenclature and connectivity checking procedures.
`A ample partial entry for the protein ribonuclease S is shown in Ta ble 2. tt The
`unique code lR S identifying thi ·entry is given in the HEADER record, along with
`the date these data were entered into the Bank, and a provisional classification ba ed
`on function , intended for future u ·ein indexing and subdividing the file. Text giving
`the name of molecule, species from which it ha been obtained, author , literature
`citation , and other general description are presented in records COMPND through
`REMARK. EQRES give
`the amino acid ·equence, and FTNOTE record are
`footnote keyed to particular r
`idue;; or atom . Record.· HELIX through TURN
`de cribe the secondary structure as stated or approved by the depositor. Record
`CRYST1 define
`th e unit cell, while ORIGX and SCALE re pectively give trans(cid:173)
`formation relating the orthogonal Ang trom co-ordinates stored in the file to those
`originally upplied by the depo ·itor (these frequently are referred to an oblique or
`non-i ometric system) and to standard crystallographic fractional co-ordinates.
`ATOM records give the IUPAC-IUB (1969) standard atom names (IUPAC-IUB,
`1970), and residue abbreviations (IUPAC-IUB, 1971), along with equence identifiers
`(cf. SEQRES, above), co-ordinate in Ang~trom units, and occupancies and thermal
`tIn addition to curren t co-ordinate entries sh own in Table 1, the Bank contains ob olete
`entries (for adenylate kinase tosyl, ex-chymotrypsin, concanavalin A, lactate d ehydrogenase, hor e
`m ethemoglobin, papain, rubredoxin, benzamidine-inhibited trypsin and pancreatic t ry psin
`inhibitor), which have been s upersed ed by later, more accurate data. These obsolete data a re
`available on s pecia l request.
`t Originally, the Bank used a 140-charaoter format, similar to that employed in the prote in
`refinemen t programs of Diamond ( 1966,1971 ). The 140-character format h as been s uperseded by
`the 0-character format.
`§ A detailed d e cription of the file f rma.ts is available from Brookhaven on request.
`Control Data. Corporation, UPDATE R eference Manual, Publication ro. 60342500, Control
`Data Corporation, Arden Hills, Minnesota, 1974.
`II G. J. B . Willia ms, unpublished . For tho 140-ch a racter data., progr·am PROIN by E. F . Meyer
`wa3 ut ilized.
`tt The file is organized in a. similar way for proteins and nucle icacids,a.lt hough certai ndiffi rencer;
`exi t, e.g. with regard to de tails of atom and residue names.
`
`PFIZER EX. 1080
`Page 5
`
`

`

`F . C. BERNSTEIN ET AL.
`
`TABLE 2
`Abbreviated sample atomic co-ordinate entry (ribonuclease S)
`
`1RNS
`
`REFEREN~F 1. F. 14, RICHARDS AND H, Wo WYCKOFFt ATLAS OF
`STRUCTw~ES FOR MOLECULAR 8 IOLOGY • VOL • 1. RIBONUCLEASE-S,
`CLARENnnN PRESS !19731.
`REFERENr.F 2. F. M. ~ICHI,RDS AND H, w. WYCKOFFt BOVINE
`PANCRE1,TTC RIBONUCLEASE• THE ENZYMES, EDITEU BY P. 0.
`BOYER• vOL• IV• THIRD EDITION• P647t AC.IIOEMIC PRESS !1971 1
`REFERENr.F 3, F. 14, RICHA~DSt H. W. WYCKOFF• w. O. CARLSON •
`N. M. ALLFWELL• B. LEE AND Yo MITSUI, PROTEIN STRUCTURE•
`RIBONUr.LEI,SE-S AND NUCLEOTIDE INTERACTIONS• COLO SPRING
`HARBOR sYMPOSIA ON QUANTITATIVE BIOLOGY• VOL. XXXVIt P35
`(1971).
`REFERENrF 4. N. M. ALLE~ELL ANO H. w. WYCKOFFt
`CRYSTAL! DGRAPHIC ANALYSIS OF THE INTERACTION OF CUPRIC
`ION WIT~ RIBONUCLEASE S• J. BIOL. CHE14•• VOL. 246t P4657
`(19711.
`REFERENr.F 5. H. w. WYCKOFFt Oo TSEHNOGLOUo A. w. HANSON,
`J. R. ~ N OXt B. LEE AND F. M. RICHAHDSt THE THREE(cid:173)
`OIMENSTnNAL STRUCTURE OF RIBONUCLEASE-So
`INTERPRETATION
`OF AN FLECTRON UENSITY MAP AT A NOMINAL RESOLUTION OF 2
`ANGSTRnMS• J, BIOL. CHEM., VOL. 24St P305 !19701.
`REFERENr.E 6. H. w. WYCKOFFt Ko O. HAROI4ANt No M. ALLEWELLt
`T. INA~A~It o. TSERNOGLOUt L• No JOHNSON AND F. M.
`RICHARns• THE STRUCTURE OF RIBONUCLEASE-<; AT 6 ANGSTROM
`RESOLUTJONt J. BIOL. CHEM., VOL. 242, P3749 !19671.
`
`HYDRDLAS~ (PHOSPHORIC DIESTERt RN.tll
`RI BONUCLFASE-S tE.c. 3.1.4.221
`BOVINE f~n~ TAURUSl PANCREAS
`F. M. RI~~AQDS AND Ho ~. WYCKOFF
`R.J. FLETTERICK AND H. ~. WYCKOFFt PRELIMINARY REFINEMENT
`OF PROTEtN COORDINATES IN RE"AL SPACEt ACTA CRYST •• VOL. A3 1t
`P698 ( 197c;l •
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`1
`2
`2 RESOLUTtnN. 2.0 ANGSTROMS,
`3
`3 REFINEM~NT. BY A STEEPEST-DESCENTS PROCEDURE, REFER TO THE
`3
`JRNL CtTATION ABOVE.
`4
`4 THIS COoRDINATE SET IS DESIGNATED 60 BY THE OEPOSITOR.
`5
`5 THE *S-pEP TIDE* !RESIDUES 1-201 WHICH FORMS A SEPARATE
`s CHAIN FRnM THE ~EMAINOER OF THE MOLECULE IS GIVEN THE
`s CHAIN InF~TIFIER S.
`1 s
`20 LYS GLU THR ALA ALA ALA LYS PHE GLU ARG GLitj HIS ME T
`2 s
`20
`.aSP SER SER THR SER ALA ALA
`104
`1
`c;ER SER SER ASN TYR CYS ASN GLitj MET MET LYS SE R ARG
`104
`.t~SN LEU THR LYS ASP ARG CYS LYS PRO VAL ASN THq PHE
`2
`3
`104 VI,L HIS GLU SER LEU ALA ASP VAL GLitj ALA VAL CYS SER
`4
`104
`t;LN LYS ASN VAL ALA CYS LYS ASN GLY GLN THR ASN CYS
`104 TYR GLN SER TYR SER THR MET SER ILE THR ASP CYS Ml G
`5
`104 ALU THR GLY SER SER LYS TYH PRO ASN CYS ALA TYR LY S
`6
`104 THR THR GLN ALA ASN LYS HIS ILE ILE VAL ALA CYS GL U
`7
`104 ALY ASN PRO TYR VAL PRO VAL HIS PHE ASP ALA SER VA L
`8
`1
`1 THE MAIN CHAIN AND MOST OF THE ASSOCIATED SIDE CHAINS AR E
`1 NOT WELL-nEFINEO IN THE REGIONS OF RESIDUES 2t 65-72 AND
`1 119-123.
`2
`2 THE MAIN CHAIN IS VERY POORLY OEFI~EO OR NOT VISIBLE AT ALL
`2 IN THE ~LECTRON DENSITY MAP
`IN THE HEGIONS OF RESIDUES 1 •
`2 18-20 • 2t-<'3 AND
`124.
`1 Hl THR c;
`3 MET S
`2 H2 ASN
`I,SN
`24
`
`13
`34
`
`HEADER
`CO"!PI>ID
`SOURCE
`.IIIJTHOR
`JRNL
`JR"'L
`JRNL
`RE14.11RK
`RE14ARK
`RE14ARI(
`REMARK
`RE14ARK
`REMARK
`REM.IIRK
`RE141,RK
`REMARK
`REMARK
`RE14ARK
`REMARK
`REMARK
`REMARK
`RE14ARK
`REMARK
`RE14ARK
`RE14ARK
`RE14ARK
`REMARK
`REMARK
`RE14ARK
`REMARK
`REMARK
`REMARK
`REMARK
`REMARK
`REMARI(
`RE14ARK
`REMARK
`REMARK
`REMARK
`REMARI(
`REMARK
`REMARK
`RE.MARK
`SEQRES
`SEQRES
`SEQRES
`SEQ RES
`SEQRES
`SEQRE"S
`SEQ RES
`SEQRES
`SE~RES
`SEQRES
`FTNOTE
`FTI>IDTE
`FTNOTE
`FTNQ TE
`FTNOTE
`FTNOTE
`FTNDTE
`FTNDTE
`HELIX
`HELIX
`
`PFIZER EX. 1080
`Page 6
`
`

`

`3 H3 SER
`51 3 Lye;
`1
`51 3 MF"T
`2
`3
`51 3 AL~
`1
`2
`3
`
`52 " Lye;
`52 " Ac;~t
`52 " HT';
`" 52 4 IIAL
`
`1 Tl 1/AL
`2 T2 ALA
`3 T3 CYS
`
`" T4 THR
`
`LETTERS TO THE EDITOR
`
`539
`
`T ABLE 2-continued
`
`""
`
`~3
`
`0 CYS
`THR
`0
`
`84
`100
`
`72
`108
`118
`
`6
`
`2
`2
`2
`2
`2
`2
`
`0
`
`3
`
`7
`
`4
`
`0
`
`6
`
`952
`
`2
`
`8
`
`10
`
`56
`1
`so ALA
`HELIX
`48
`0
`41 HIS
`SHEET
`"' ASN
`87 -1
`79
`THR
`SHEET
`104 -1 N ASP
`96 LYS
`SHEET
`64
`0
`61 ALA
`SHEET
`1;3
`75 -1 N VAL
`0 CYS
`SER
`71
`SHEET
`111 -1 N TYH
`73
`0 VAL
`1 OS GLIJ
`SHEET
`109
`0 ALA
`N
`1/AL
`124 -1
`1/AL
`116
`SHEET
`PSEUDO 3/10 HELIX
`57
`54 VAL
`TURN
`PSEUDO 3/10 HELIX
`59
`56 SER
`TURN
`BETW SlRNOS 1t2 OF SHEET 52
`61!
`65 GLY
`TURN
`END OF STRANO 2 OF SHEET 51
`90
`SER
`87
`TURN
`97.150 90.00 90,00 120.00 p 31 2 1
`44.650
`44ofl50
`CRYSTl
`o.oooooo
`1.0000no o.oooooo o.oooooo
`ORIGX1
`o.oooooo
`1,000000 o.oooooo
`o.oooon 11
`ORIGX2
`u.oooooo
`o.ooooo" o.oooooo 1.000000
`ORIGX3
`o.oooooo
`,012931
`o.oooooo
`.0223<11;
`SCALE1
`o.oooooo
`o.oooooo
`,025861
`o.oooonn
`SCALE2
`o.oooooo
`.010293
`o.oooooo o.oooooo
`SCALE3
`7.914 20.202 1.00 o.oo
`-15.394
`1
`Lye; 5
`1 N
`ATOM
`7.636 18.730 1.00 o.oo
`-15.145
`2
`CA
`1
`Lye: 5
`ATOM
`3 c
`6.107 18.763 1.00 o.oo
`-14.982
`c;
`Lye;
`1
`ATOM
`" 0
`5.351 19.732 1.00 o.oo
`-15.145
`1
`Lye; 5
`ATOM
`8.24'+ 19.185 1.oo o.oo
`-13.872
`c;
`1
`LYe;
`5 CB
`ATOM
`7.6!>'> 18.794 1.00 o.oo
`-12.693
`c;
`Lye;
`1
`CG
`6
`ATOM
`~~~·~·~·~·~·~·~·~·~·~·~·~·~·~·~~·~·~·~·~·~·~~·~·~·~·~·~·~·~·~~·~·~·~·~·~·~·~·~·~
`ATOM
`927 N
`Ac;p
`121
`-6.795
`-9.247
`7.034 1,00 0,00
`1
`ATOM
`928 CA Ac;p
`121
`-5.813
`-9.425
`5,935 1.00 0,00
`1
`ATOM
`929 C
`Ac;p
`121
`-6.217 -10.156
`4.7R9 1.00 0,00
`1
`930
`0
`Ac;p
`121
`-5.828
`-9.850
`3.652 1,00 0,00
`1
`ATO~
`931 C8 Ac;p
`121
`-4.529 -10.015
`6.6~8 1.00 0,00
`1
`ATO~
`ATOM
`932 CG Ac;p
`121
`-3.471
`-9,503
`5,687 1.00 0,00
`1
`ATOM
`933
`001 Ac;p
`121
`-3.320
`-R.082
`5.636 1.00 0,00
`1
`ATOM
`934 002 Ac;p
`121
`-2.718 -10.333
`4,799 1.00 0,00
`1
`ATOM
`935 N
`A1 a
`122
`-7,049 -11.201
`5.013 1,00 0,00
`1
`ATOM
`936 CA
`AI . A
`122
`-7.965 -12.086
`4,084 1.00 0,00
`1
`ATOM
`937 C
`ALA
`122
`-8,554 -13.331
`4.724 1.00 0,00
`1
`ATOM
`938
`0
`At.A
`122
`-8.495 -13.636
`5,925 1.00 0,00
`1
`ATOM
`939 CB
`ALA
`122
`-6.991 -12.510
`2.881 1.00 0,00
`1
`ATOM
`940 N
`5F"CI
`123
`-8.885 -13.915
`3,717 1,00 0,00
`1
`ATOM
`941
`CA
`SF'P
`123
`-9,758 -15.15!>
`3.627 1.00 0,00
`1
`ATOM
`942 C
`5FP
`123
`-8.915 -16.127
`2.8RO 1,00 0,00
`1
`ATOM
`943
`0
`SF'Q
`123
`-8.372 -15,812
`1,810 1.00 0.00
`1
`ATOM
`944 CB
`5FP
`123
`-10.877 -14.659
`2,597 1,00 0,00
`1
`ATOM
`945 OG
`5FP
`123
`-10,157 -14,035
`1,530 1,00 0,00
`1
`ATOM
`946 N
`VAL
`124
`-8.R45 -17.415
`J,438 1,00 0,00
`2
`ATOM
`947
`CA Val
`124
`-8,591 -18,490
`2,596 1,00 0,00
`2
`ATOM
`948 C
`VAL
`124
`-9.235 -18.381
`1,209 1,00 0,00
`2
`ATOM
`949
`0
`Vat.
`124
`-8,580 -17.735
`,377 1,00 0,00
`2
`950 CB Val
`124
`-8.937 -19.929
`3,162 1,00 0,00
`2
`ATO~
`ATOM
`951 CG1 VAL
`124
`-9.135 -20,905
`2.012 1,00 0.00
`2
`952 CG2 VAL
`124
`-7,784 -20,573
`4.226 1.00 0,00
`2
`ATO~
`ATOM
`953 OXT Val
`124
`-10,419 -19,165
`1,046 1,00 0.00
`2
`II Al~
`TER
`954
`124
`195
`CO"'ECT
`196
`fl44
`311
`CONECT
`312
`7;>9
`447
`CONECT
`448
`A44
`CONECT
`498 497
`<;4'l
`CONECT
`549 498
`o:;4R
`CONECT
`644
`196
`643
`CONECT
`729 312
`7;:>Fl
`CONECT
`844 448
`A43
`MASTER
`36
`1 n
`E"'!O
`
`PFIZER EX. 1080
`Page 7
`
`

`

`540
`
`F. C. BERNSTEIN ET A L.
`
`motion factors, if these latter data are provided. Within each residue, atoms arc
`ordered in a standard manner, starting with the backbone (N-Ca-C- 0) and
`proceeding in increasing remoteness from the alpha carbon atom along t he side-chain.
`Ca has been encoded CA, C13 as CB , et c. Where the sequence is known, but atoms have
`not been located in th e structure analysis, gaps have been left in th e atom serial
`numbers, to allow for future insertion. A TER recmd d enotes an explicit chain(cid:173)
`terminating residue. CONECT records give bond connectivity, for all atoms where
`the covalent connectivity is not specified completely by the atom name and order of
`serial numbers within th e entry (i.e. th e primary structure of standard residues).
`CONECT records may also be used to denote hydrogen bond and alt bridge inter(cid:173)
`actions. Each entry is terminated with a MASTER record, which gives checksums of
`the number of records, broken down by record t ype, a nd an END of d ata record.
`
`(c) Services
`The activities of the Protein Data Bank are to collect and standardize data from
`laboratories engaged in the analysis of macromolecular structures, and to distribute
`these data within the scientific community . As a service to depositors, data are
`checked for errors of a clerical nature but no ex haustive verification is attempted.
`The Data Bank is located at Brookhaven National La boratory and input of data to
`the Bank and general maintenance functions are carried out at Brookhaven t.
`
`TABLE 3
`Protein Data Bank activities
`
`Co-ordinate
`en t ries
`h eld at
`end of year
`
`Co-o rdinate entries distributed
`Broo k-
`Cam-
`haven
`bridge
`
`Tokyo T otal
`
`L a boratories receiv ing data
`Bt"Ook-
`Cam-
`h aven
`bridge
`
`T o kyo T otal
`
`15
`17
`40
`69
`
`106
`99
`5 13
`1920
`
`30
`102
`241
`600
`
`136
`201
`754
`2766
`
`14
`14
`31
`47
`
`2
`6
`6
`14
`
`246
`
`16
`20
`37
`70
`
`9
`
`Y ear
`
`1973
`1974
`1975
`1976
`
`Duplicate copies of t he Brookhaven mast er file are maintained at Cambridge and
`Tokyo. Data are available on magnetic t ape for public distribution, from Brookhavent
`(to laboratories in the Americas) , Tokyo (Japan) , and Cambridge (Europe and world(cid:173)
`wide) . The data are also available in a limited way within t he United States over the
`Crystallographic Computing Network (Koetzle et al. , 1975). R etrieval programs to
`access data in the file have been described (Meyer, 1974 ; M. Tasumi, personal com(cid:173)
`munication). These efforts represent modest initial attempts at interactive access:
`up to the present the Protein Data Banl{ has served a lmost exclusively the demands of
`off-line users. A sta tistical summary of the Bank's activities is given in Table 3.
`These statistics show rapid growth , both in number of holdings and in requests filled.
`t D etails of operations a r·e a nnounced period ically in a Newsl<'tte r· (cu r·rcnt i ~s u c is number 3,
`November 1976). Cop ies may b e obtained fr·om Brookhave n.
`t R equests should be accompa nied wit h a new 2400 ft, reel of magnetic tape, and a ch eck or
`purchase order for U.S. $34.30 made to the order of Brookh aven National L aboratory, to cover
`postage and ha ndling. This charge is subject to change in the future.
`
`PFIZER EX. 1080
`Page 8
`
`

`

`LETTER S TO THE EDITOH
`
`541
`
`(d) Future developments
`In the future, it is hoped to expand the flCope of the Protein Data Bank to make
`available co-ordinates for standard structural t ypes (e.g . .x-helix, RNA double(cid:173)
`stranded helix) and representative computer programs of utility in the study of
`macromolecular structures. A small number of programs will be written to calculate
`useful quantities d erived from the co-ordinates (namely torsion angles, wire-model
`bender angles, full covalent connectivities, etc.). In addition to tills software, the
`Bank will undertake to distribute contributed programs, provided that documentation
`is deposited in machine-readable form with source code.t In order to facilitate use of
`atomic co-ordinate d ata to assemble models from standardized parts, it is intended
`to offer a " model-builder 's kit", to consist of header information, a compa.ct list of
`co-ordinates to 0·1 A preeision, and torsion angles. This kit would be distributed
`principally in the form of printed listings, but also would be available on magnetic tape.
`As the size of the Bank grow'l, possibilities for wide interactive access to the atomic
`co-ordinate dat a v'ia a network will become more attractive. This type of acces would
`increase the fil e's utility, particularly to those outside the fields of crystallography
`and analysis of protein a nd nucleic acid conformations, by removing the necessity
`for repeated development of retrieval program . For example, graphics terminals
`could be used to draw pictures of macromolecules for research or instructional purposes .
`Network access will be a topic of continued exploration in th e next few years.
`Suggestions regarding possible future improvements in Protein Data Bank services
`wil l be appreciated by th e authors.
`
`The late V\Talter C. H amil to n was one of t he founders of t his project. H elen M. B erman
`participated in the initial organiza tion of the Data B ank a nd also was active in preparation
`of some of t he first data entries as were Betty H . D avis and D a niel D. J ones . Numerous
`individuals h ave offered helpful suggestion s a nd crit icism s : H erbert J. B ernst ein , David
`M. Blow, JohnS . Coggins, H ober t Diam ond, Anthon y C. T. N orth , Mi chael G. H ossmann ,
`and David G . W atson. H,ich ard J. F eldmann generously has tran sferred numerous atomic
`co-ordinate en tries originall y collected for inclusion in AMSOM. The m embers of th e
`Protein D a t a B a nk Adv isory Group, D avid R. D avies, K enneth N eet and Frederic M.
`Hichards h ave overseen oul' operati ons and engaged in m any u seful discussion s.
`This work was p erformed under t he auspices of the U.S. Energy H esearch and D evelop(cid:173)
`ment Administra tion and suppor ted b y the U.S. N ation al Science F otmda tion under grants
`AG-370, GJ 33248X , DCH- 75- 07702 , and P CM7 5- 18956.
`
`Chemistry D ep artment
`Brookhaven N a tional L ab oratory
`Upton, N.Y. 11973 , U .S.A.
`
`University Chemi cal L ab oratory
`Lensfield Hoad, Cambridge CB2 JEW , Engla nd
`
`University of T oky o
`Hongo, T okyo, J·apa n
`
`FRANCES C. BER N STEIN
`THOMAS F. KOETZLE t
`G RAHEll'lE J. B. WILLIAMS
`EDGAR F . M E YER, JR§
`M ICHAEL D. BRICE
`JOHN H,. HODGERS
`OLGA K ENNARD t,-r
`
`TAKEHIKO SHI111ANOUCHI
`MrTsu o T Asmn t
`
`Received 21 F ebruary 1977
`t The Bank will ass ume n o r esponsibili ty for checkou t or correction of errors in s uch deposited
`programs.
`t To wh om corresp ondence sh ould be addressed .
`§Permanent a ddress : D epa rt ment of Biochemistry and Biophysics, T exas A & M University ,
`College Stat ion , Texas 77843. R esearch colla borato r at Brookh aven N ational Laboratory .
`~ E x terna l staff, Medical R esearch Cow1cil.
`
`PFIZER EX. 1080
`Page 9
`
`

`

`542
`
`F. C. BERNSTEIN ET AL.
`
`REFERENCES
`Allen, F. H. , K ennard, 0. , Motherwell, W. D . S., Town , W . G. & Watson, D . G. (1973).
`J . Chem. Doc. 13, 119- 123.
`Diamond, R. (1966). A cta Crystallogr. 21 , 253- 266.
`Diamond, R. (1971). Acta Crystallogr. sect. 4, 27 ,436- 452.
`F eldmann, R. J. (1977). Atlas of Macromolecular S tructu1·e on Microfiche, Tracor Jitco
`Inc., Rockville.
`IUPAC-IUB Commission on Biochem ical Nomenclature (1970) . J . Biol. Chem. 245 , 6489-
`6497 .
`IUPAC-IUB Commission on Biochemi cal Nomenclature (1971). J . Biol. Chern . 247 ,
`977- 983.
`K ennard, 0 ., Watson , D . G. & T own, W. G. (1972). J . Chern. Doc. 12 , 14-19.
`Koetzle, T. F., Andrews, L. C., Bernstein , F. C. & Bernstein , H . J . (1975). In Computer,
`Networking and Chemistry (Lykos, P. , ed.), ACS Symposium Series, vol. 19, p. 1,
`American Chemical Society, W ashington.
`Meyer, E. F. (1974). B iopolymers, 13, 419- 422.
`Protein Data Bank (1971) . Nature New Biol. 233, 223.
`Protein Data Bank (1973). Acta Crysta.llogr. sect. B, 29, 1746.
`
`PFIZER EX. 1080
`Page 10
`
`