J. Mol. Biol. (1977) 112, 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- 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. ~-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures. The Protein Data Bank~ (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 10 v 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- ruination of Inorganic Crystal Structures (BIDICS):~ 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- 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. I. D. Brown, Bond Index to the Determination of Inorganic Crystal Structures, MeMaster University, Hamilton, Ontario, Canada, L8S 4M1. § American Society for Testing Materials, 1916 Race St., Philadelphia, PA. 19103, U.S A. 535
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 1 of 8
`
`

`
`636 F. C. BERNSTEIN ET AI,. TaBL~ 1 Protein data bank holdings IDENT CODE IADK IADH 2RDH 2CHQ 3CHA l FAB IREI 1CPV 2CPV 3CPV 1CAB ICQC ICPA ICHG 2CHA 3CNA tBSC ICYT 2CYT ICYC I C2C 155C IEST IFDX IFXH IGCH IGPD 2MHB 1DHB 1HHB | FDH ILHB IYHX IHIP 2LDH 36OH ILYZ 2LYZ 3LYZ 4LYZ 5LYZ 6LYZ IMDH IMBH 2PBH 3MBH 3PT I 8PAP 2PAP 3PAP 4PAP 5PAP GPAP 7PAP IPGK 2PGK IPAB IRNS 2R>@I ISNS ISGB ISBT 2SBT 1 SOD ITLN 2TLN 1SRX 1 "ilia 2THR 3TNA ITIM IPTN 2PTB IPTC BLANK R B D H P R DEPOSITOR MOLECULE ADEHYLATE KIHASE G. SCHULZ ALCOHOL DEHYDROGENASE (ADP-RIB) C.-I. BRAHDEH ALCOHOL DEHYDROGENASE (ORTHOPHEN) C.-I. BRAHDEH ALPHA-CHYMOTRYF'SlN (TOSYL) D. BLOU ALPHR-CHYMOTRYPSIH A, TULIHSKY ANTIGEN BINDING FRAGIIZHT (NEll) R. POLJRK BENCE-JOHES II~HOGLOBULIH RE1 O. EPP, R. HUBER CALCIUM-BIHDIHG PARVALBUMIN SET 6A R. KRETSIHGER CALCIUM-BINDING PARVALBUMIH SET 6H R. KRETSlHGER CALCIUM-BINDING PQRVALBUMIH SET El R. KRETSINGER CARBOHIC ANHYDRASE B K. KANNAN CARBONIC RNHYDRASE C K. KAHNAN CARBOXYPEPTIDASE A II. LIPSCOMB CHYHO1RYPSIHOGEH J. KRAUT COHCAHAVALIN A G, REEKE. G. EDE/..~IAH COHCAHRVALIN R K, HRRDI'tClH CYTOCHROHE B5 F, S. MATHEhlS CYTOCHROME C (ALBACORE. OXIDIZED) R. DICKERSOH CYTOCHROME C (ALBACORE, REDUCED) R. DICKERSON CYTOCHROHE C (BONITO, HEART) M, KAKUDO CYTOCHROME C2 J. KRQUT CYTOCHROHE C550 R. TIMKOVICH ELASTASE H. UATSON FERREDOXIH L. JENSEN FLAVODOXIN (CLOSTRIDIUM MP) M, LUDQIG GA~'~-CHYMOTRYPSIN COHEH,DAVIES,SILVERTON GLYCERRLDEHYDE-3-P-DEHYI)ROGEHRSE (LOBSTR) M. ROSSI'IAHH HEMOGLOBIN (HORSE, AOUO MET) HEMOGLOBIN (HORSE, DEOXY) HEMOGLOBIH (HUHAIIo DEOXY) M. HEMOGLOBIH (HUMRH. FETAL. DEOXY) J. HEMOGLOB IH (LAI'PREY) W, HEXOKINASE (YEAST) BIII T, HIGH POTENTIAL IRON PROTEIH J. LACTATE DEHYDROGEHASE M. LACTATE DEHYDROGEHASE/NAD/PYRUVATE M. LYSOZYME (HEN EGG-UHITE, SET U2) R, LYSOZYME (HEN EGG-UHITE, SET RS5D) R. LYSOZYME (HEH EGG-UNITE, SET RS6Q) R. LYSOZWE (HEH EGG-I~IITE, SET RsgA) R. LYSO7YME (HEN EGG-WHITE, SET RSI2A) R. LYSOZYI'E (HEN EGG-WHITE, SET RS16) R. MALATE DEHYDROGEHASE L. MYOGLOBIH (SPERM WHALE) H. MYOGLOBILI (SPERM UHALE, MET) T. MYOGLOBIH (SPERM UHALE, DEOXY) T. PAHCREATIC TRYPSIN INHIBITOR R. PAPAIN. NATIVE J. PAPAII'I (ACE-ALA-ALA-PHE-ALA, CYS-25) J. PAPAIH (CYS DERIV OF CYS-25) J. PAPAIN (OXIDIZED CYS-25) J. PAPAIH (TOS-LYS, CYS-25) J. PRPAItl (BZOXY-GLY-PHE-GLY, CYS-25) J. PAPA IH (BZOXY-PNE-ALR, CYS-25) J. PHOSPHOGLYCERATE KINASE (YEAST) H. PHOSPIIOGI.YCERATE KIHASE (HORSE) P. PREALBUMIH (HUI~H, PLASI'R) S. R IBOHUCLEASE S H. RUBREDOXIN L. STAPHYLOCOCCAL NUCLERSE F. STREPTOMYCES GRISEUS PROTEINASE B h. SUBTIL ISlH BPN" J. SUBTIL IS IN NOVO J. SUPEROXIDE b ISMUTASE J. THERHOLY5 IN (UNREFINED) B, THERMDLYS IN (REFINED) TH IOREDOXIN TRANSFER RNA (YEAST, PHE) TRANSFER RNA (YEAST, PHE) TRANSFER RHA (YEAST, PHE) TRIOSE PHOSPHATE ISOMERASE TRYPSIH (HRTI~A~, PHO) TRYPSIN(BEHZAMIDIHE INHIBITED, PHT) TRYPSIII/TRYPSIN INHIBITOR COHPLEX STATUS CODES STANDARD ENTRY AVAILABLE FOR DISTRIBUTION ALPHA CARBON ATOMS ONLY BACKBONE BNLY NEll DATA HAS BEEN PROMISED NEll EHTRY WITH DEPOSITOR FOR APPROVAL IN PREPARATION REPLACES AH OUT OF DATE PARAMETER SET STATUS CODE P N LADNER, HEIDHER, PERUTZ RP M. PERUTZ, G. FERMI PERUTZ, G. FERMI FRIER HEHDR I CKSOH STEITZ B KRRUT ROSSMQHH PD ROSSMRHH PD D I AMOND P D I AMOHD P D IAMOHD P D IQMOND P D IAr~HD P D IAMOHD P BAHASZQK A WATSON TAKAHO TAKRHO IiUBER R DRENTH R DRENTH DRENTH DREHTH DREHTH DREHTH DREHTH IJATSOI'I R EVANS. D, PHILLIPS B OATLEY, D. PHILLIPS gYCKOFF JENSEN HI) A. COTTON, E. HRZEN JAMES A KRAUT DRENTH AND D. RICHARDSON R I~TTHEllS B. HFITTHEI~3 B.-O. SODERBERG R J. SUSSI"IANo S.-H. KIM H M. SUHDARAL INGRM P JACK, LADHER, KLUG P I. IJILSON, D. PHILLIPS FEHLHAMI'ER • BODE. SCHUAGER N FEHLHAYtlER • BODE, SCHWRGER RN BODE ET RL. H
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 2 of 8
`
`

`
`LETTERS TO THE EDITOR 537 on data abstracted from scientific publications. The Bank contains 77 atomic co- ordinate entries for 47 macromolecules (Table 1),~ and 13 sets of structure factors and phases. The atomic co-ordinate entries, which include descriptive text and partial bond connectivities, conform to a uniform format (see below), but the structure factors and phases are stored in the format received from depositors. All co-ordinate entries are referred to depositors for verification, before being made available publicly through the Bank. (b) Record structure of atomic co-ordinate entries Atomic co-ordinate entries consist of records each of 80 characters.$ 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 is added by the library-file management program UPDATE¶ used to maintain the file on the Brookhaven CDC CYBER 70/76 computing system. In order to facilitate retrieval of data from the file, the first four characters of each record define the unique record type, and the syntax of each record is independent of the order of records within any entry for a particular macromolecule. (In the master file, this order is always fixed.) Atomic co-ordinate data contributed by depositors are processed into the standard format with program I~IACi~OL, H which also subjects the data to certain nomenclature and connectivity checking procedures. A sample partial entry for the protein ribonuclease S is shown in Table 2.~ The unique code 1RNS identifying this entry is given in the HEADER record, along with the date these data were entered into the Bank, and a provisional classification based oa function, intended for future use in indexing and subdividing the file. Text giving the name of molecule, species from which it has been obtained, authors, literature citations, and other general description are presented in records G01~IPND through RElVIARK. SEQRES gives the amino acid sequence, and FTI~0TE records are footnotes keyed to particular residues or atoms. Records HELIX through TURN describe the secondary structure as stated or approved by the depositor. Record CRYST1 defines the unit cell, while 0RIGX and SCALE respectively give trans- formations relating the orthogonal l~mgstrSm co-ordinates stored in the file to those originally supplied by the depositor (these frequently are referred to an oblique or non-isometric 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 sequence identifiers (cf. SEQRES, above), co-ordinates in ~mgstrSm units, and occupancies and thermal t In addition to current co-ordinate entries shown in Table 1, the Bank contains obsolete entries (for adenylate kinase tosyl, ¢¢-ehymotrypsin, coneanavalin A, lactate dehydrogenase, horse methemoglobin, papain, rubredoxln, benzamidine-inhibited trypsin and pancreatic trypsin inhibitor), which have been superseded by later, more accurate data. These obsolet~e data are available on special request. Originally, the Bank used a 140-character format, similar to that employed in the protein refinement programs of Diamond (1966,1971). The 140-character format has been superseded by the 80-character format. § A detailed description of the file formats is available from Brookhaven on request. ¶ Control Data Corporation, UPDATE Reference Manual, Publication 1~o. 60342500, Control Data Corporation, Arden Hills, Minnesota, 1974. I[ G. J. B. Williams, unpublished. For the 140-character data, program PROIN by E. F. Meyer wa~ utilized. t j- The file is organized in a similar way for proteins and nucleic acids, although certain differences exist, e.g. with regard to details of atom and residue names.
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 3 of 8
`
`

`
`F. C. BERNSTEIN ET AL. TA.BL:E 2 Abbreviated sam1~le atomic co-ordinate entry (ribonuclease S) HEADER COMPNO SOURCE AUTHOR JRNL JRNL JRNL REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REHARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK REMARK SEQRES SEORES SEORES SEORES SEORES SEORES SEORES SEORES SEORES SEORES FTNOTE FTNOTE FTNOTE FTNOTE FTNOTE FTNOTE FTNOTE FTNOTE HELIX HELIX 1 1 I 1 1 1 1 1 1 1 1 2 2 3 3 3 4 4 5 5 5 5 1 2 1 2 3 6 5 6 7 8 1 1 1 1 2 2 2 2 1 2 HYDROLASF (aHOSPHORIC DIESTER, RNA) 01-APR-73 IRNS RIBONUCLFASE-S (B.C. 3.1.4.22) BOVINE (mnS TAURUS) PANCREAS F. M. RI~HAqDS AND H. ~. WYCKOFF R.J. FLETTEQICK AND H. W. WYCKOFF, PRELIMINARY REFINEMENT OF PROTETM cOORDINATES IN REAL SPACE* ACTA CRYST., VOL. A31+ P698 (19Tq). 1 1REFERENcF 1. F. M. RICHARDS AND H. M. WYCKOFF+ ATLAS OF 1 $TRUCTIIDES FOR MOLECULAR BIOLOGY+ VOL. 1. RIBONUCLEASE-S+ 1 CLARENnnM PRESS (1973). 1REFERENcp 2e F. M. RICHAROS AND H. W. WYCKOFF+ BOVINE 1 PANCREATTC RIBONUCLEASE+ THE ENZYMES+ EDITED BY P. O. 1 BOYER, vOLe IV+ THIRD EDITION+ P6~7+ ACADEMIC PRESS (1971) 1REFERENcF 3. F. q. RICHARDS+ H. We WYCKOFF. W. 6. CARLSON+ l N. M. ALL,WELL+ B. LEE AND Y. MITSUI, PROTEIN STRUCTURE+ 1 RIBONU~LEASE-S AND NUCLEOTIOE INTERACTIONS, COLD SPRING 1 HARBOR ~yMPOSIA ON QUANTITATIVE BIOLOGY, VOL. XXXVI+ P35 1 (1971). I REFERENcF 4. N. M. ALLEWELL ANO H, W. WYCKOFF+ 1 CRYSTALLOGRAPHIC ANALYSIS OF THE INTERACTION OF CUPRIC ION MITq RIBONUCLEASE S, J. 8IOLe CHEM.+ VqL. 246, P~657 (1971). REFEREN~F B. H. W. WYCKOFF+ D. TSEHNOGLOU+ A. W. HANSON, J. R. xNOX, B. LEE AND F. M. RICHARDS, THE THREE- DIMENST~NAL STRUCTURE OF RIBOMUCL~ASE-S. INTERPRETATION OF AN FLECTRON DENSITY MAP AT A NOMINAL RESOLUTION OF 2 ANGSTRnNs. J. BIOL. CHEM.+ VOL. 2~5+ P30S (1970). REFEREN~ 8. H. W. WYCKOFF+ K. D. HAROHAN, N. N. ALLE~ELL, T. INARA~I+ 0. TSERNOGLOU+ L* N. JOHNSON ANO F, M. RICHARDq+ THE STRUCTURE OF RIBONUCLEASE-R AT 6 ANGSTROM RESOLUTTON+ J. BIOL. CHEM., VOLe 2~Z+ P3749 (1967). RESOLUTInN. 2.0 ANGSTROMS. REFINEMENT. BY A STEEPEST-DESCENTS PROCEOUREe REFER TO THE JRNL CTTATION ABOVE. THIS CO~DDINATE SET IS DESIGNATED bO BY THE OEPOSITOR. THE *S-DEPTIDE o (RESIOUES 1-20) WHICH FORMS A SEPARATE CHAIN F~nq THE REMAINOER OF THE MOLECULE IS GIVEN THE CHAIN InF~TIFIER S. S 20 LYS GLU THR ALA ALA S 20 AS~ SER SER THR SER 104 qE~ SER SER ASN TYR 104 ~SN LEU THR LYS ASP 104 vAL HIS GLU SER LEU 104 ~LN LYS ASN VAL ALA 104 TYR GLN SER TYR SER 104 RLU THR GLY SER SER 104 THR THR GLN ALA ASN 104 RLY ASN PRO TYR VAL ALA LYS PHE GLU ARG GLN HIS MET ALA ALA CYS ASN GLN MET MET LYS SER ARG ARG CYS LYS PRO VAL ASN THq PHE ALA ASP VAL GLN ALA VAL CYS SEN CYS LYS ASN GLY GLN THR ASN CYS THR M~T SER ILE THR ASP CYS ARG LYS TYH PRO ASH CYS ALA TYR LYS LYS HIS ILE ILE VAL ALA CY5 GLU PRO VAL HIS PHE ASP ALA SEN VAL THE MAIM CHAIN AND MOST OF THE ASSOCIATED SIDE CHAINS ARE NOT WELL.DEFINED IN THE REGIONS OF RESIDUES Z, 65-72 AND 119-123. THE MAIN CHAIN IS VERY POORLY OEFINEO OR NOT VISIBLE AT ALL IN THE rLECTRON DENSITY MAP IN THE HEGIONS OF RESIDUES 1, 1B-20,21-23 AND 12&. H1THR q 3 MET S 13 1 H2 ASN 26 ASN 34 1
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 4 of 8
`
`

`
`LETTERS TO THE EDITOR 539 TABLE 2--continued HELIX 3 H3 SER 50 ALA SHEET 1 51 3 Lv~ 41 HIS SHEET 2 S1 3 MFT 79 THR SHEET 3 $1 3 ALA 96 LYS SHEET 1 $2 4 LY~ 61 ALA SHEET 2 $2 4 Aq~ 71 SER SHEET 3 $2 4 HI~ 105 OLU SHEET 4 S2 4 V~ L 116 VAL TURN 1 TI VAL 54 VAL TURN 2 T2 ALA 56 SER TURN 3 T3 CY5 65 GLY TURN 4 T4 THR 87 SER 56 1 ¢8 0 87 -1 N ASN 64 0 CYS 104 -1" N ASP 83 0 THR 64 0 75 -1 N VAL 63 0 CYS 1il -1 N TYR 73 0 VAL 124 -1 O ALA 109 N VAL 57 PSEUDO 3/10 HELIX 59 PSEUDO 3/10 HELIX 68 90 84 100 7~ 108 118 8ETW SIRNOS 1,2 OF SHEET $2 END OF 5TRANO 2 OF SHEET S1 CRYSTI 44,650 ORIGXI ORIGX2 ORIGX3 SCALE1 SCALE2 SCALE3 ATOM ATOM ATOM ATOM ATOM ATOM 44.~50 97.150 90.00 90.00 120.00 P 31 2 1 6 l,O000On 0.000000 0.000000 0.000000 0.00000~ 1,000000 0.000000 0.000000 0.00000~ 0.000000 1.000000 0.000000 .0223o6 ,012931 0.000000 0,000000 0.0000~0 ,025861 0.000000 0.000000 O.O000OO 0.000000 .010293 0,000000 1 N Ly~ S 1 -15.394 7,914 20.202 1.00 0,00 2 2 CA Ly~ S 1 -15.145 7.636 18.730 1.00 0,00 2 3 C Lyq R 1 -14.982 6.107 18.763 1.00 0.00 2 4 0 Lyq S 1 -15.145 5.351 19.732 1.00 0.00 2 5 CB Lv~ ~ 1 -13,872 8,244 18.185 1,00 0,00 2 6 CO Lyq ~ 1 -12.693 7,654 18.794 1.00 0.00 2 ATOM ATOM ATOM ATOM ATOq ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM ATOM TER COMECT 196 195 ~46 CONECT 312 311 7~9 CONECT 448 447 ~44 CONECT 498 497 ~A9 CONECT 549 498 ¢4R COMECT 644 196 643 CONECT 729 312 778 CONECT 844 448 R~3 MASTER 36 In EMO 927 N Acp 121 928 CA ACD 121 929 C AMp 121 930 0 A~p 121 931 C8 AMp 121 932 CG AMp 121 933 001A~o 121 934 002 A~p 121 935 N Ai.a 122 936 CA AIs 122 937 C ALa 122 938 0 AI.A 122 939 C8 ALA 122 940 N 5~R 123 941 CA Sro 123 942 C SFp 123 943 0 SFQ 123 944 CB SF~ 123 945 OG S~ 123 946 N VAL 124 947 CA VAL 124 948 C VA L 124 949 0 Vat. 124 950 CB VAL 124 951 col VAL 124 952 CO2 VAL 124 953 OXT VAL 124 95¢ VAt. 124 -6.795 -9.247 7.034 1.00 0.00 1 -5,813 -9.425 5.935 1.00 0.00 1 -6,217 -10.156 4.789 1.00 0.00 1 -5.828 -9,850 3.652 1.00 0.00 1 -4.529 -10.015 6.6~8 1.00 0.00 1 -3,471 -9.503 5.687 1.00 0.00 I -3.320 -8.082 5.636 1.00 0.00 1 -2,718 -10.333 4.799 1.00 0.00 1 -7.049 -11.201 5.013 1.00 0,00 1 -7,865 -12.086 4.084 1.00 0.00 1 -8.554 -13.331 4.724 1.00 0.00 1 -8.495 -13.636 5.925 1.00 0.00 1 -6.991 -12.510 2.881 1.00 0.00 1 -8.885 -13.915 3.717 1.00 0.00 1 -9.758 -15.155 3.627 1.00 0.00 1 -8.915 -16.127 2.880 1.00 0.00 1 -8.372 -15.812 1.810 1.00 0.00 1 -10.877 -14.659 2.597 1.00 0,00 1 -10.157 -14.035 1.530 I.O0 0.00 1 -8.845 -17.415 3.438 1.00 0.00 2 -8,591 -18,490 2,596 1,00 0,00 2 -9.235 -18.381 1,209 1.00 0.00 2 -8.580 -17,735 .377 1.00 0.00 2 -8.937 -19,929 3.162 1.00 0.00 2 -9.135 -20.905 2.012 1,00 0.00 2 -7.784 -20,573 4.226 1.00 0.00 Z -10.419 -19.165 1.046 1.00 0.00 2 0 3 7 4 0 6 952 2 8 10
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 5 of 8
`
`

`
`540 F.C. BERNSTEIN ET AL. motion factors, ff these latter data are provided. Within each residue, atoms are ordered in a standard manner, starting with the backbone (N--Ca--C--O) and proceeding in increasing remoteness from the alpha carbon atom along the side-chain. Ca has been encoded CA, C~ as CB, etc. Where the sequence is known, but atoms have not been located in the structure analysis, gaps have been left in the atom serial numbers, to allow for future insertion. A TER record denotes an explicit chain- 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 the entry (i.e. the primary structure of standard residues). CONECT records may also be used to denote hydrogen bond and salt bridge inter- actions. Each entry is terminated with a MASTER record, which gives checksums of the number of records, broken down by record type, and an END of data 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 exhaustive verification is attempted. The Data Bank is located at Brookhaven National Laboratory and input of data to the Bank and general maintenance functions are carried out at Brookhavent. TA.BLE 3 Protein Data Bank activities Year Co-ordinate Co-ordinate entries distributed Laboratories receiving data entries Brook- Cam- Brook- Cam- held at haven bridge Tokyo Total end of year haven bridge Tokyo Total 1973 15 106 30 -- 136 14 2 -- 16 1974 17 99 102 -- 201 14 6 -- 20 1975 40 513 241 -- 754 31 6 -- 37 1976 69 1920 600 246 2766 47 14 9 70 Duplicate copies of the Brookhaven master file are maintained at Cambridge and Tokyo. Data are available on magnetic tape for public distribution, from Brookhaven$ (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and world- wide). The data are also available in a limited way within the United States over the Crystallographic Computing Network (Koetzle et al., 1975). Retrieval programs to access data in the file have been described (Meyer, 1974; M. Tasumi, personal com- munication). These efforts represent modest initial attempts at interactive access: up to the present the Protein Data Bank has served ahnost exclusively the demands of off-line users. A statistical summary of the Bank's activities is given ill Table 3. These statistics show rapid growth, both in number of holdings and in requests filled. Details of operations are announced periodically in a Newsletter (current issue is number 3, November 1976). Copies may be obtained from Brookhaven. Requests should be accompanied with a new 2400 ft reel of magnetic tape, and a cheek or purchase order for U.S. $34.30 made to the order of Brookhaven National Laboratory, to cover postage and handling. This charge is subject to change in the future.
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 6 of 8
`
`

`
`LETTERS TO THE EDITOR 541 (d) Future developments 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. ~-helix, RNA double- 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 derived from the co-ordinates (namely torsion angles, wire-model bender angles, full covalent connectivities, etc.). In addition to this 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 data to assemble models from standardized parts, it is intended to offer a "model-builder's kit", to consist of header information, a compact list of co-ordhlates to 0.1 A precision, and torsion angles. This Idt would be distributed principally in the form of printed listings, but also would be available on magnetic tape. As the size of the Bank grows, possibilities for wide interactive access to the atomic co-ordinate data via a network will become more attractive. This type of access would increase the file's utility, particularly to those outside the fields of crystallography and analysis of protein and nucleic acid conformations, by removing the necessity for repeated development of retrieval programs. 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 the next few years. Suggestions regarding possible future improvements in Protein Data Bank services will be appreciated by the authors. The late Walter C. Hamilton was one of the founders of this project. Helen M. Berman participated in the initial organization of the Data Bank and also was active in preparation of some of the first data entries as were Betty R. Davis and Daniel D. Jones. Numerous individuals have offered helpful suggestions and criticisms: Herbert J. Bernstein, David M. Blow, John S. Coggins, Robert Diamond, Anthony C. T. North, Michael G. Rossmann, and David G. Watson. Richard J. Feldmann generously has transferred numerous atomic co-ordinate entries originally collected for inclusion in AMSOM. The members of the Protein Data Bank Advisory Group, David R. Davies, Kenneth Neet and Frederic l~I. Richards have overseen our operations and engaged in many useful discussions. This work was performed under the auspices of the U.S. Energy Research and Develop- ment Administration and supported by the U.S. National Science Foundation under grants AG-370, GJ 33248X, DCR-75-07702, and PCM75-18956. Chemistry Department Brookhaven National Laboratory Upton, N.Y. 11973, U.S.A. University Chemical Laboratory Lensfield Road, Cambridge CB2 IEW, England University of Tokyo Hongo, Tokyo, Japan Received 21 February 1977 FRANCES C. BERNSTEIN THOMAS F. KO~TZnE:~ GRAHEME J. B. WIL~MS EDGAR F. MEYER, JR§ MICHAEL D. BRICE JOHN R. RODGERS OLGA KENNARD$¶ TAKEmKO SHIMANOUCHI MITSUO TASUMI~ t The Bank will assume no responsibility for checkout or correction of errors in such deposited programs. :~ To whom correspondence should be addressed. § Permanent address: Department of Biochemistry and Biophysics, Texas A & M University, College Station, Texas 77843. Research collaborator at Brool~haven National Laboratory. ¶ External staff, Medical Research Council.
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 7 of 8
`
`

`
`542 F.C. BERNSTEIN E T A L. REFERENCES Allen, F. H., Kennard, O., Motherwell, W. D. S., Town, W. G. & Watson, D. G. (1973). J. Chem. Dec. 18, 119-123. Diamond, R. (1966). Aet~ CrystaUogr. 21, 253-266. Diamond, R. (1971). Acta Cryst~llogr. sect. A, 27, 436-452. Feldmann, R. J. (1977). Atlas of Maeromoleeu[ar ~ructure on Microfiche, Tracor Jitco Inc., RockviUe. IUPAC-IUB Commission on Biochemical Nomenclature (1970). J. Biol. Chem. 245, 6489- 6497. IUPAC-IUB Commission on Biochemical Nomenclature (1971). J. Biol. Chem. 247, 977-983. Kennard, O., Watson, ]3. G. & Town, W. G. (1972). J. Chem. Doe. 12, 14-19. Koetzle, T. F., Andrews, L. C., Bernstein, F. C. & Bernstein, H. J. (1975). In Computer, iVetworld~l and Chemistry (Lykos, P., ed.), ACS Symposium Series, vol. 19, p. 1, American Chemical Society, Washington. Meyer, E. F. (1974). Biopolymers, 13, 419-422. Protein Data Bank (1971). 1Vature New Biol. 233, 223. Protein Data Bank (1973). Aeta Crys~llogr. sect. B, 29, 1746.
`
`PETITIONER'S EXHIBITS
`
`Exhibit 1080 Page 8 of 8