HEADER ZN-BINDING PROTEIN 13-MAY-97 1WJB TITLE SOLUTION STRUCTURE OF THE N-TERMINAL ZN BINDING DOMAIN OF HIV-1 TITLE 2 INTEGRASE (D FORM), NMR, 40 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POTENTIAL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ZN-BINDING PROTEIN, AIDS, POLYPROTEIN, HYDROLASE, ASPARTYL PROTEASE, KEYWDS 2 ENDONUCLEASE EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR G.M.CLORE,M.CAI,M.CAFFREY,A.M.GRONENBORN REVDAT 4 22-MAY-24 1WJB 1 REMARK REVDAT 3 02-MAR-22 1WJB 1 REMARK LINK REVDAT 2 24-FEB-09 1WJB 1 VERSN REVDAT 1 13-MAY-98 1WJB 0 JRNL AUTH M.CAI,R.ZHENG,M.CAFFREY,R.CRAIGIE,G.M.CLORE,A.M.GRONENBORN JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL ZINC BINDING DOMAIN OF JRNL TITL 2 HIV-1 INTEGRASE. JRNL REF NAT.STRUCT.BIOL. V. 4 567 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9228950 JRNL DOI 10.1038/NSB0797-567 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED USING THE SIMULATED REMARK 3 ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. REMARK 3 229, 129 - 136 USING THE PROGRAM XPLOR 3.1 (BRUNGER) REMARK 3 MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. REMARK 3 (1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON REMARK 3 CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. REMARK 3 SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL REMARK 3 DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, REMARK 3 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177) REMARK 3 REMARK 3 THE 3D STRUCTURE OF THE N-TERMINAL DOMAIN OF HIV-1 REMARK 3 INTEGRASE WAS SOLVED BY REMARK 3 MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR REMARK 3 IS BASED ON 640 EXPERIMENTAL RESTRAINTS (PER MONOMER): REMARK 3 (A) INTRASUBUNIT: 156 SEQUENTIAL (|I-J|=1), 137 MEDIUM REMARK 3 RANGE (1 < |I-J| >=5) AND 47 LONG RANGE (|I-J| >5) REMARK 3 INTERRESIDUE, AND 15 INTRARESIDUE APPROXIMATE INTERPROTON REMARK 3 DISTANCE RESTRAINTS; 14 DISTANCE RESTRAINTS FOR 7 REMARK 3 HYDROGEN BONDS; 92 TORSION ANGLE (45 PHI, 5 PSI, 30 CHI1 REMARK 3 AND 12 CHI2) RESTRAINTS; 36 THREE-BOND HN-HA COUPLING REMARK 3 CONSTANT RESTRAINTS; 97 (50 CALPHA AND 47 CBETA) 13C REMARK 3 SHIFT RESTRAINTS. REMARK 3 (B) 28 INTERSUBUNIT INTERPROTON DISTANCE RESTRAINTS. REMARK 3 (C) 23 AMBIGUOUS INTERPROTON DISTANCE RESTRAINTS THAT CAN REMARK 3 ARISE FROM INTRA AND/OR INTERSUBUNIT INTERACTIONS. REMARK 3 REMARK 3 THE STRUCTURES IN THIS ENTRY ARE THE 40 SIMULATED ANNEALING REMARK 3 STRUCTURES THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA REMARK 3 STRUCTURES HAS NO MEANING. THE LAST LETTER COLUMN REMARK 3 SIGNIFIES THE SUBUNIT (A OR B). RESIDUES 47 - 55 ARE REMARK 3 DISORDERED. REMARK 4 REMARK 4 1WJB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177207. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX600; DMX500; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR MODIFIED MODIFIED REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 GLU A 10 -149.61 -158.31 REMARK 500 1 GLU A 13 -155.98 -100.38 REMARK 500 1 PRO A 30 -18.10 -40.23 REMARK 500 1 GLN A 44 -74.53 -76.21 REMARK 500 1 LYS A 46 -79.91 -90.00 REMARK 500 1 ALA A 49 -92.98 -69.66 REMARK 500 1 GLU B 10 -149.55 -158.68 REMARK 500 1 GLU B 13 -155.84 -100.30 REMARK 500 1 PRO B 30 -18.11 -40.22 REMARK 500 1 GLN B 44 -74.43 -76.17 REMARK 500 1 LYS B 46 -79.83 -90.00 REMARK 500 1 ALA B 49 -93.10 -69.79 REMARK 500 2 HIS A 12 72.12 -69.61 REMARK 500 2 GLU A 13 -151.19 -101.08 REMARK 500 2 PRO A 30 -18.95 -40.73 REMARK 500 2 ALA A 49 93.51 52.11 REMARK 500 2 MET A 50 -164.77 -115.61 REMARK 500 2 HIS A 51 110.81 83.53 REMARK 500 2 GLN A 53 -167.64 52.83 REMARK 500 2 HIS B 12 71.99 -69.63 REMARK 500 2 GLU B 13 -151.12 -100.92 REMARK 500 2 PRO B 30 -18.91 -40.69 REMARK 500 2 ALA B 49 93.40 51.94 REMARK 500 2 MET B 50 -164.20 -115.21 REMARK 500 2 HIS B 51 111.38 82.67 REMARK 500 2 GLN B 53 -167.86 52.77 REMARK 500 3 HIS A 12 75.67 -64.14 REMARK 500 3 PRO A 30 -18.77 -40.07 REMARK 500 3 GLN A 44 -70.76 -79.49 REMARK 500 3 MET A 50 -95.86 -70.09 REMARK 500 3 HIS B 12 76.49 -63.71 REMARK 500 3 PRO B 30 -18.62 -40.27 REMARK 500 3 GLN B 44 -70.73 -79.94 REMARK 500 3 MET B 50 -95.97 -70.21 REMARK 500 4 GLU A 13 -149.52 -101.52 REMARK 500 4 PRO A 30 -18.16 -41.85 REMARK 500 4 ALA A 49 173.95 -49.63 REMARK 500 4 GLU B 13 -149.74 -101.64 REMARK 500 4 PRO B 30 -18.47 -41.24 REMARK 500 4 ALA B 49 173.44 -49.92 REMARK 500 5 HIS A 12 75.59 -64.47 REMARK 500 5 PRO A 30 -15.74 -44.76 REMARK 500 5 GLN A 44 -71.29 -79.55 REMARK 500 5 HIS B 12 74.70 -63.71 REMARK 500 5 PRO B 30 -15.05 -44.89 REMARK 500 5 GLN B 44 -71.57 -79.71 REMARK 500 6 GLN A 44 -76.03 -72.60 REMARK 500 6 ALA A 49 -140.17 -60.80 REMARK 500 6 GLN B 44 -75.89 -72.49 REMARK 500 6 ALA B 49 -140.33 -60.88 REMARK 500 REMARK 500 THIS ENTRY HAS 287 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 56 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 ND1 REMARK 620 2 HIS A 16 ND1 107.4 REMARK 620 3 CYS A 40 SG 125.2 118.8 REMARK 620 4 CYS A 43 SG 93.7 105.5 100.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 56 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 12 ND1 REMARK 620 2 HIS B 16 ND1 107.4 REMARK 620 3 CYS B 40 SG 125.2 118.9 REMARK 620 4 CYS B 43 SG 93.8 105.4 100.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 56 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 56 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WJA RELATED DB: PDB DBREF 1WJB A 1 55 UNP P12497 POL_HV1N5 716 770 DBREF 1WJB B 1 55 UNP P12497 POL_HV1N5 716 770 SEQRES 1 A 55 PHE LEU ASP GLY ILE ASP LYS ALA GLN GLU GLU HIS GLU SEQRES 2 A 55 LYS TYR HIS SER ASN TRP ARG ALA MET ALA SER ASP PHE SEQRES 3 A 55 ASN LEU PRO PRO VAL VAL ALA LYS GLU ILE VAL ALA SER SEQRES 4 A 55 CYS ASP LYS CYS GLN LEU LYS GLY GLU ALA MET HIS GLY SEQRES 5 A 55 GLN VAL ASP SEQRES 1 B 55 PHE LEU ASP GLY ILE ASP LYS ALA GLN GLU GLU HIS GLU SEQRES 2 B 55 LYS TYR HIS SER ASN TRP ARG ALA MET ALA SER ASP PHE SEQRES 3 B 55 ASN LEU PRO PRO VAL VAL ALA LYS GLU ILE VAL ALA SER SEQRES 4 B 55 CYS ASP LYS CYS GLN LEU LYS GLY GLU ALA MET HIS GLY SEQRES 5 B 55 GLN VAL ASP HET ZN A 56 1 HET ZN B 56 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 LEU A 2 ALA A 8 1 7 HELIX 2 2 LYS A 14 SER A 17 1 4 HELIX 3 3 TRP A 19 PHE A 26 1 8 HELIX 4 4 PRO A 30 SER A 39 1 10 HELIX 5 5 ASP A 41 GLN A 44 1 4 HELIX 6 6 LEU B 2 ALA B 8 1 7 HELIX 7 7 LYS B 14 SER B 17 1 4 HELIX 8 8 TRP B 19 PHE B 26 1 8 HELIX 9 9 PRO B 30 SER B 39 1 10 HELIX 10 10 ASP B 41 GLN B 44 1 4 LINK ND1 HIS A 12 ZN ZN A 56 1555 1555 2.10 LINK ND1 HIS A 16 ZN ZN A 56 1555 1555 2.18 LINK SG CYS A 40 ZN ZN A 56 1555 1555 2.32 LINK SG CYS A 43 ZN ZN A 56 1555 1555 2.26 LINK ND1 HIS B 12 ZN ZN B 56 1555 1555 2.10 LINK ND1 HIS B 16 ZN ZN B 56 1555 1555 2.19 LINK SG CYS B 40 ZN ZN B 56 1555 1555 2.32 LINK SG CYS B 43 ZN ZN B 56 1555 1555 2.26 SITE 1 AC1 4 HIS A 12 HIS A 16 CYS A 40 CYS A 43 SITE 1 AC2 4 HIS B 12 HIS B 16 CYS B 40 CYS B 43 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1