ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS Vol. 185, No. 2, January 30, pp. 584-591, 1978

The Protein

Data Bank: A Computer-based Archival Macromolecular Structures

File for

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 Iland (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 st.ores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried orlt at Brookhaven National Laboratory. All data stored in the I3ank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan) 3 and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies arc 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. a-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolocu1a.r structures.

The

Data Bank? (1971,1973) was established in 1971 as a computer-based 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 st,ructures has grown to the point where some lo7 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, (Allen et al., 1973) e.g. the Bibliographic (Kennard et al., 1972) and Structural Data Files for organic and organometallic compounds, the Atlas of Macromolecular Structure on Microfiche (AMSOM) (Feldmann, 1977), the Bond Tndex to the Deterand the Powder Diffraction He. $ mination of Inorganic Crystal Structures (BIDICS)$ Protein

archival

The

Protein

Data Bank covers atomic co-ordinat,es, structure factors and phases from diffraction studies of macromolecules. Since most of this information is not the Bank depends for comprehensivegenerally published in the primary literature, 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 7 Protein Data Bank is a misnomer of historical nucleic acid. t I. D. Brown, Bond Index to the Determination University, Hamilton, Ontario, Canada, L8S 4Ml. J American Society for Testing Materials, 1916 584 0003-9861/78/1852-0584$02.00/O Reprinted from J. Mol.

Biol.

112,

5939-5941

(1977).

origin,

since

of Inorganic Race

St.,

the file

now

Crystal

Philadelphia,

contains Structures,

PA.

19103,

entries

for

McMaster U.S

A.

a

585

1DEN7 CODE

PlOLECULE

1FlDK 1fiDH ZADH 2CHA 3CHR 1FAB IREI ICPV XPV 3CPV 1CkB 1CHC 1CPQ ICHG 2CNi) 3cNa 1 B5C 1C:‘T 2CYT 1C’I’C IC2C 155C IEST IFDX ;;s;

DEPOS G.

IIIDENYL~ITE K INASE FlLCOHOL DEHYDROGENASE (ADP-RIB) FtLCOHOL DEHYDPOGENf4SE (ORTHOPHEM) hLPHFI-CHL’I’IOTRYPS IN (TOSM) @LPHil-CHYflilTR’,.PS IN fit-LTIGEII BIEIDING FRFlGMENT (NEW) BEtICE-JOI+ES II-lIIUtlOGLOl?UL IN RE I CGLC IUrl-8 IIID ING PARVQI-RIUI1Ib’ SET CHLCIUI~-BIH~III~G PAPVIALEUIIIN SET T:RLC ILtkl-ElIiD IIIG PtiRVALBUIlIN SET

IIHSE

L.JHALE > UHhLE, MET) LtHfiLE, DEOXY) ITIC TI;“I’F’SIII ItlHlElTOR IIlil’I’;‘E rliC~-tilt-kLF!-PtlE-ALL. CYS-25)

I r>I; I: 2F’GK 1PFlB 1RNS 2RXII 1SNS ISGB ISBT

SCHULZ BRANDEN BRaI tr,rzrr 6iOW TUL lN5KY POLJ&K EPP R YI:BLF KU& lil!XFI KRETS3thER hut TS I I-rGER hkrltlri’l I:: KG’lt!HN w. LlP~CQ!lB J. KciiLli ;~ RtEu-EC 2. EL?F! .liN . HYRi;lRt~l S I IriTtlEiJS k* DiCI,ERSOti R: D I&ERSON n. l;aKUDO J. KRRUT R. TIIII’OV~CH H. WliTSOtl L. JEllSEll 11 . L U D W I G COHE~t.Il~VIES.SILVERTOt~ TR 1 M. FOSSI IfvIN LRDtlER. HEIDNER. PER+jTZ PERUTZ. G. FEPIlI F’EPUTZ. G. FERIII FP IER yii~~cl 0. PHILLIPS ORTLEY. D. PHILLIPS WYCKOFF JENSEN i%&TTON. E. HRZEN E-ZD: I?. R. 0 R: R. ;.

FEF’FEId:< I tl FLQVODC1:,.:IIi [CLClSTR ID 1lJM MP) GWII lt+CH’i’llOTRYPS ltl GL‘~‘iEPALDEti‘,‘DE-3-P-DEHYDROGENQSE(LOBS HEtlOI;LOBItI tHOF:SE, fi@UO MET) HEll01;LOBltl (HCJPSE. DEOXY) IiEtl~-G..UC III tHUtlHl -1 I iJiOXY) HEI‘IIlGLHC IN ~HW’lAI ‘I. FETRL. DEOXY) HEIII!I;LCIE Itl 1,LrilIF’PEY) IiE:::OI; If WSE 1“TEliSTl I3 I I I HIGH F’CITEtIT. 114. IROtI FPUTEIH I ;>I-TATF ,‘DPOGEtIASE I’I’F’DGEtlliSE,‘t~~D,‘PYRUVFtTE W2) RS5D) HSCFO RSSR) US 12FI) III EGG-LJHITE. SET RSl6)

l&D ;‘I1HE 1flHE I IHHB 1FDH 1LHB 1 iHX 1HIP ?LDH 3LIjH ILYZ ZL‘I’Z 3 L ‘iZ 4L ‘I’Z 5L ‘.I’2 6L’r’Z IIIDH 1MEI-I 21 IEN 31lBll 3PTI BPkP dPHP 3PI4P .IPfiP 5FliP y&f;

: 0

KRQUT DRENTH &iFTfli$

:2;; IYLN 2TLtI lSF!X ITllA 5% t;:‘;l 2PTB 1PTC

PH7) .EX STATUS

BLCINK i? E f;

STFlTUS CODE

I TOR

COIIES STfitlDRRD ENTRY AVFI ILFtBLE FOR DlSTR IEUTION FiLPHG CRRBOtI FlTOFlS ONLY BACl>BONE ONLY NEW DATR Ht9S BEEN PROMISED IIELJ EtlTRY WITH DEPOSITOR FOR APPROVAL It1 PCEPhRATI0t-I REPLQCES At-l OUT OF DATE PI?RQtlETER SET

cl R

R RP

R R

ND A

I CHflRDSON

HATTHEWS B.-O. SODERBERG J. SUSSWN. S.-H. KIM H. SltNDfiRFIL 1MGRtl JRCK. LfiDNER. KLUG I a WILSON. D. PHILLIPS FEHLHRtU-IER. BODE. SCHLJfiGER FEHLHAIY~IER. BODE. SCHWAGER BODE ET BL.

67

THE

PROTEIN

DATA

587

BANK

TABLE 2 Abbreviaied HYDROLASF

COMPND SOURCE AI~THOR JRNL JRNL JRNL REMARK REMARK REHARU REMARK REMARK REHARK REMARK REHhRK REMARK REMARU REYARK REHhRK REMARK REMARK

QIBONUCLfASE-S

REUARK REMARK REYARK REMARK REMARK REMARK REYARK REMARK REMARK RENARK 4EHARK REHARK REMARK REMARK REMARK REMARK REHARK REHARU REMARK REMARK RENARK

SEQRES SEORES SEQRES SEQRES SEQRES SEQRES SEQRES SEQRES SEQRES SEQRES FTMOTE FTYOTE FTYOTE FTNOTE FtNOtE FTt.IOtE FTNOTE FTNOTE HELIX HELIX

atomic

co-ordinate

entry (ribonuclease

h’)

DKESTERv RN41 Ol-4PR-73 1RYS 3-1.4.22) BOVINE i-: rlumhrxr 3, November 1976). Copic:i may be obtained from Brookhaven. tape, an(l a chrrk 01 $ Requests should be accompanied with a new 2 400 ft. rwl of magnetic purchase order for U.S. $34.30 made to the order of Brookha\ren National I,aboratory, to CO\YI postage and handling. This charge is subject to change in the fnturc.

THE

PROTEIN

DATA

591

BANK

KEFEHENCES Allen,

F.

H.,

Kennard,

J. Chem. Dot.

O.,

Motherwell,

W.

D.

S., Town,

11’. G.

& IVatson,

D.

G.

(1973).

13, 119-123.

Diamond, R. (1966). Acta Crystallogr. 21, 253 266. Diamond, R. (1971). Acta Cqstallogr. sect. A, 2’7, 436 -452. Feldmann, R. J. (19771. Atlas of ~1Zacronaolec~~Zar Structcwe or{- ,Ilicrojche, Tracer Jitco Inc., Rockville. IUPAC-IUB Cornmissiwl on 13iocllertlir:i+l S(,lnt,trc~l~ttIrr,r (1 970). .I. Hid. Chem. 245, 6489 6497. IUPAC-IUB Commission or1 Hiot:I~c:~t~i~al X(,lnc,rlc.Iat,rlr.~? (I 97 1). .J. Hiol. Chew. 247, 977m 983. Kennard, O., Watson, I). G. & Tows, I\‘. G. (I!ji2). .I. Chem. IAx. 12, 14- 19. Koetzle, T. F., Andrews, L. C., Bernstein, F. C. & Hernsteirl, H. J. (1975). In Computer, Networking and Chemistry (Lykos, P., ed.), ACS Symposium Series, l-01. 19, p. I, American Chemical Society, Washingtoll. Meyer, E. F. (1974). Biopolymers, 13, 419%422. Protein Data Bank (1971). Nalure A’eu Biol. 233, 223. Prot’ein Data Rank (1973). Acta Crystallogr. sect. R, 29, 1746.

The Protein Data Bank: a computer-based archival file for macromolecular structures.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS Vol. 185, No. 2, January 30, pp. 584-591, 1978 The Protein Data Bank: A Computer-based Archival Macromolecul...
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