HEADER TRANSFERASE 01-JUL-11 3ZT4 TITLE SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE TITLE 2 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CORE CATALYTIC DOMAIN, RESIDUES 56-212; COMPND 5 EC: 2.7.7.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: INHIBITOR BOUND TO THE LEDGF SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 12721; SOURCE 4 STRAIN: TYPE 1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS TRANSFERASE, AIDS EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.NEWMAN,D.I.RHODES,N.VANDERGRAAFF,G.LE,E.D.JONES,J.A.SMITH, AUTHOR 2 J.A.V.COATES,N.THIENTHONG,O.DOLEZAL,J.H.RYAN,G.P.SAVAGE,C.FRANCIS, AUTHOR 3 J.J.DEADMAN REVDAT 3 20-DEC-23 3ZT4 1 REMARK REVDAT 2 01-AUG-12 3ZT4 1 JRNL REVDAT 1 18-JUL-12 3ZT4 0 JRNL AUTH T.S.PEAT,D.I.RHODES,N.VANDERGRAAFF,G.LE,J.A.SMITH,L.J.CLARK, JRNL AUTH 2 E.D.JONES,J.A.V.COATES,N.THIENTHONG,J.NEWMAN,O.DOLEZAL, JRNL AUTH 3 R.MULDER,J.H.RYAN,G.P.SAVAGE,C.L.FRANCIS,J.J.DEADMAN JRNL TITL SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS INTEGRASE IDENTIFIED BY FRAGMENT JRNL TITL 3 SCREENING AND STRUCTURE BASED DESIGN JRNL REF PLOS ONE V. 7 40147 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22808106 JRNL DOI 10.1371/JOURNAL.PONE.0040147 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.I.RHODES,T.S.PEAT,N.VANDEGRAAFF,D.JEEVARAJAH,G.LE, REMARK 1 AUTH 2 E.D.JONES,J.A.SMITH,J.A.COATES,L.J.WINFIELD,N.THIENTHONG, REMARK 1 AUTH 3 J.NEWMAN,D.LUCENT,J.H.RYAN,G.P.SAVAGE,C.L.FRANCIS, REMARK 1 AUTH 4 J.J.DEADMAN REMARK 1 TITL STRUCTURAL BASIS FOR A NEW MECHANISM OF INHIBITION OF HIV-1 REMARK 1 TITL 2 INTEGRASE IDENTIFIED BY FRAGMENT SCREENING AND REMARK 1 TITL 3 STRUCTURE-BASED DESIGN. REMARK 1 REF ANTIVIR.CHEM.CHEMOTHER. V. 21 155 2011 REMARK 1 REFN ISSN 0956-3202 REMARK 1 PMID 21602613 REMARK 1 DOI 10.3851/IMP1716 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 18108 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 981 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1358 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2335 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.02000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.229 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.322 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2635 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 22 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3605 ; 2.105 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 48 ; 1.404 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 5.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 109 ;30.069 ;25.229 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 452 ;15.583 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.438 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 394 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2119 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 26 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3ZT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290048891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19132 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 61.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3NF7 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN WAS CONCENTRATED TO REMARK 280 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM REMARK 280 DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, REMARK 280 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5., PH 5.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.18633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.37267 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -88.3 KCAL/MOL 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 56 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 139 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN A, PHE 185 TO HIS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 56 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 139 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN B, PHE 185 TO HIS REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 SER A 49 REMARK 465 HIS A 50 REMARK 465 HIS A 51 REMARK 465 HIS A 52 REMARK 465 HIS A 53 REMARK 465 HIS A 54 REMARK 465 HIS A 55 REMARK 465 SER A 56 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 LYS A 211 REMARK 465 GLU A 212 REMARK 465 MET B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 SER B 49 REMARK 465 HIS B 50 REMARK 465 HIS B 51 REMARK 465 HIS B 52 REMARK 465 HIS B 53 REMARK 465 HIS B 54 REMARK 465 HIS B 55 REMARK 465 GLY B 189 REMARK 465 GLY B 190 REMARK 465 ILE B 191 REMARK 465 GLY B 192 REMARK 465 THR B 210 REMARK 465 LYS B 211 REMARK 465 GLU B 212 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 202 OE1 GLN B 209 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 171 CG HIS A 171 CD2 0.056 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 GLN B 146 0.61 -57.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 A 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 A 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 B 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 B 1215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HYV RELATED DB: PDB REMARK 900 HIV INTEGRASE CORE DOMAIN COMPLEXED WITH TETRAPHENYLARSONIUM REMARK 900 RELATED ID: 1HYZ RELATED DB: PDB REMARK 900 HIV INTEGRASE CORE DOMAIN COMPLEXED WITH A DERIVATIVE OFTETRAPHENYL REMARK 900 ARSONIUM. REMARK 900 RELATED ID: 3ZSO RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DESIGN REMARK 900 RELATED ID: 3ZSQ RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSR RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSV RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSW RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSX RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSY RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZSZ RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT0 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT1 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT2 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN REMARK 900 RELATED ID: 3ZT3 RELATED DB: PDB REMARK 900 SMALL MOLECULE INHIBITORS OF THE LEDGF SITE OF HIV TYPE 1 INTEGRASE REMARK 900 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DRUG DESIGN DBREF 3ZT4 A 56 212 UNP Q76353 Q76353_9HIV1 56 212 DBREF 3ZT4 B 56 212 UNP Q76353 Q76353_9HIV1 56 212 SEQADV 3ZT4 MET A 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 GLY A 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER A 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER A 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS A 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER A 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZT4 ASP A 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZT4 HIS A 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQADV 3ZT4 MET B 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 GLY B 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER B 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER B 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 HIS B 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZT4 SER B 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZT4 ASP B 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZT4 HIS B 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQRES 1 A 167 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER PRO SEQRES 2 A 167 GLY ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS SEQRES 3 A 167 VAL ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE SEQRES 4 A 167 GLU ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR SEQRES 5 A 167 ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL SEQRES 6 A 167 LYS THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER SEQRES 7 A 167 THR THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS SEQRES 8 A 167 GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SER GLN GLY SEQRES 9 A 167 VAL ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE SEQRES 10 A 167 GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA SEQRES 11 A 167 VAL GLN MET ALA VAL PHE ILE HIS ASN HIS LYS ARG LYS SEQRES 12 A 167 GLY GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL SEQRES 13 A 167 ASP ILE ILE ALA THR ASP ILE GLN THR LYS GLU SEQRES 1 B 167 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER PRO SEQRES 2 B 167 GLY ILE TRP GLN LEU ASP CYS THR HIS LEU GLU GLY LYS SEQRES 3 B 167 VAL ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE SEQRES 4 B 167 GLU ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR SEQRES 5 B 167 ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL SEQRES 6 B 167 LYS THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER SEQRES 7 B 167 THR THR VAL LYS ALA ALA CYS TRP TRP ALA GLY ILE LYS SEQRES 8 B 167 GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SER GLN GLY SEQRES 9 B 167 VAL ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE SEQRES 10 B 167 GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA SEQRES 11 B 167 VAL GLN MET ALA VAL PHE ILE HIS ASN HIS LYS ARG LYS SEQRES 12 B 167 GLY GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL SEQRES 13 B 167 ASP ILE ILE ALA THR ASP ILE GLN THR LYS GLU HET SO4 A1211 5 HET SO4 A1212 5 HET SO4 A1213 5 HET ACY A1214 4 HET EDO A1215 4 HET ZT2 A1216 23 HET ZT2 A1217 23 HET SO4 B1210 5 HET SO4 B1211 5 HET SO4 B1212 5 HET ACY B1213 4 HET ZT2 B1214 23 HET ZT2 B1215 23 HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM ZT2 5-[(E)-(2-OXO-2,3-DIHYDRO-1H-INDEN-1-YLIDENE)METHYL]-1, HETNAM 2 ZT2 3-BENZODIOXOLE-4-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 6(O4 S 2-) FORMUL 6 ACY 2(C2 H4 O2) FORMUL 7 EDO C2 H6 O2 FORMUL 8 ZT2 4(C18 H12 O5) FORMUL 16 HOH *103(H2 O) HELIX 1 1 THR A 93 TRP A 108 1 16 HELIX 2 2 ASN A 117 SER A 123 1 7 HELIX 3 3 SER A 123 GLY A 134 1 12 HELIX 4 4 PRO A 145 ARG A 166 1 22 HELIX 5 5 ASP A 167 ALA A 169 5 3 HELIX 6 6 HIS A 171 LYS A 186 1 16 HELIX 7 7 SER A 195 GLN A 209 1 15 HELIX 8 8 SER B 56 PRO B 58 5 3 HELIX 9 9 THR B 93 TRP B 108 1 16 HELIX 10 10 ASN B 117 SER B 123 1 7 HELIX 11 11 SER B 123 GLY B 134 1 12 HELIX 12 12 PRO B 145 ARG B 166 1 22 HELIX 13 13 ASP B 167 ALA B 169 5 3 HELIX 14 14 HIS B 171 LYS B 186 1 16 HELIX 15 15 SER B 195 GLN B 209 1 15 SHEET 1 AA 5 ILE A 84 ILE A 89 0 SHEET 2 AA 5 LYS A 71 HIS A 78 -1 O VAL A 72 N ILE A 89 SHEET 3 AA 5 ILE A 60 LEU A 68 -1 O GLN A 62 N VAL A 77 SHEET 4 AA 5 THR A 112 HIS A 114 1 O THR A 112 N TRP A 61 SHEET 5 AA 5 LYS A 136 GLU A 138 1 O LYS A 136 N VAL A 113 SHEET 1 BA 5 ILE B 84 ILE B 89 0 SHEET 2 BA 5 LYS B 71 HIS B 78 -1 O VAL B 72 N ILE B 89 SHEET 3 BA 5 ILE B 60 LEU B 68 -1 O GLN B 62 N VAL B 77 SHEET 4 BA 5 THR B 112 HIS B 114 1 O THR B 112 N TRP B 61 SHEET 5 BA 5 LYS B 136 GLU B 138 1 O LYS B 136 N VAL B 113 CISPEP 1 GLY A 192 GLY A 193 0 -12.12 SITE 1 AC1 4 THR A 66 HIS A 67 LYS A 159 HOH A2040 SITE 1 AC2 5 GLY A 94 SER A 123 THR A 124 THR A 125 SITE 2 AC2 5 HOH A2020 SITE 1 AC3 5 LYS A 71 GLU A 170 HIS A 171 LEU A 172 SITE 2 AC3 5 HOH A2045 SITE 1 AC4 5 GLU A 85 GLU A 87 PHE A 100 HOH A2013 SITE 2 AC4 5 ARG B 107 SITE 1 AC5 5 HIS A 67 ALA A 91 GLU A 92 HOH A2016 SITE 2 AC5 5 ZT2 B1215 SITE 1 AC6 10 GLN A 168 ALA A 169 GLU A 170 HIS A 171 SITE 2 AC6 10 THR A 174 MET A 178 GLN B 95 TYR B 99 SITE 3 AC6 10 THR B 125 ALA B 129 SITE 1 AC7 14 TYR A 83 HIS A 185 ARG A 187 SER A 195 SITE 2 AC7 14 GLY A 197 GLU A 198 VAL A 201 GLY B 106 SITE 3 AC7 14 ARG B 107 TRP B 108 PRO B 109 LYS B 111 SITE 4 AC7 14 ILE B 204 ILE B 208 SITE 1 AC8 5 THR B 66 HIS B 67 LYS B 136 LYS B 159 SITE 2 AC8 5 HOH B2033 SITE 1 AC9 5 LYS B 71 ARG B 166 HIS B 171 LEU B 172 SITE 2 AC9 5 HOH B2039 SITE 1 BC1 5 GLY B 94 SER B 123 THR B 124 THR B 125 SITE 2 BC1 5 HOH B2016 SITE 1 BC2 8 ARG A 107 HOH A2013 GLU B 85 ALA B 86 SITE 2 BC2 8 GLU B 87 PHE B 100 LYS B 103 LEU B 104 SITE 1 BC3 12 GLN A 95 TYR A 99 THR A 125 ALA A 129 SITE 2 BC3 12 TRP A 132 HOH A2021 GLN B 168 ALA B 169 SITE 3 BC3 12 GLU B 170 HIS B 171 THR B 174 MET B 178 SITE 1 BC4 10 ARG A 107 ILE A 204 ILE A 208 EDO A1215 SITE 2 BC4 10 TYR B 83 HIS B 185 ARG B 187 SER B 195 SITE 3 BC4 10 GLY B 197 VAL B 201 CRYST1 71.058 71.058 66.559 90.00 90.00 120.00 P 31 6 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 0.014073 0.008125 0.000000 0.00000 SCALE2 0.000000 0.016250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015024 0.00000