HEADER TRANSFERASE 01-JUL-11 3ZT2 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.L.FRANCIS, AUTHOR 3 J.J.DEADMAN REVDAT 3 20-DEC-23 3ZT2 1 REMARK REVDAT 2 01-AUG-12 3ZT2 1 AUTHOR JRNL REVDAT 1 11-JUL-12 3ZT2 0 JRNL AUTH T.S.PEAT,D.I.RHODES,N.VANDEGRAAFF,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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 39230 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2070 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2440 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.4410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2318 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 138 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.736 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2612 ; 0.031 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3576 ; 2.791 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 327 ; 6.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;33.097 ;25.238 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;15.022 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;11.407 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 389 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2094 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1535 ; 1.690 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2490 ; 2.613 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1077 ; 3.358 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1069 ; 4.813 ; 4.500 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 3ZT2 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_1290048889. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-09 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 : 41795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 61.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 40MM TRIS PH 8.0, 250MM NACL, 30MM MGCL2, 5MM DTT REMARK 280 AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0M AMMONIUM SULFATE, REMARK 280 100MM 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 22.32633 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 44.65267 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: 4730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.9 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 GLY A 192 REMARK 465 THR A 210 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 SER B 56 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 O HOH A 2024 O HOH A 2026 1.82 REMARK 500 O1 SO4 A 1212 O HOH A 2044 2.00 REMARK 500 O HOH B 2006 O HOH B 2016 2.04 REMARK 500 N SER B 57 O HOH B 2001 2.07 REMARK 500 OE1 GLU B 87 O ACT A 1213 2.09 REMARK 500 N SER A 57 O HOH A 2001 2.13 REMARK 500 OE1 GLU A 87 OXT ACT A 1214 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 VAL A 79 CB VAL A 79 CG2 0.131 REMARK 500 TYR A 83 CD1 TYR A 83 CE1 0.134 REMARK 500 GLU A 87 CG GLU A 87 CD 0.110 REMARK 500 ALA A 175 CA ALA A 175 CB 0.135 REMARK 500 TYR B 83 CD1 TYR B 83 CE1 0.097 REMARK 500 GLU B 87 CG GLU B 87 CD 0.095 REMARK 500 GLU B 157 CG GLU B 157 CD 0.095 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 PRO A 142 56.71 -67.15 REMARK 500 PRO B 142 63.09 -69.29 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 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 A 1216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 A 1217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1210 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1211 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1212 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZT2 B 1214 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 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: 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 REMARK 900 RELATED ID: 3ZT4 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 3ZT2 A 56 212 UNP Q76353 Q76353_9HIV1 56 212 DBREF 3ZT2 B 56 212 UNP Q76353 Q76353_9HIV1 56 212 SEQADV 3ZT2 MET A 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 GLY A 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER A 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER A 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS A 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER A 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZT2 ASP A 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZT2 HIS A 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQADV 3ZT2 MET B 46 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 GLY B 47 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER B 48 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER B 49 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 50 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 51 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 52 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 53 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 54 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 HIS B 55 UNP Q76353 EXPRESSION TAG SEQADV 3ZT2 SER B 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3ZT2 ASP B 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3ZT2 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 A1210 5 HET SO4 A1211 5 HET SO4 A1212 5 HET ACT A1213 4 HET ACT A1214 4 HET ACT A1215 4 HET ZT2 A1216 23 HET ZT2 A1217 23 HET SO4 B1210 5 HET SO4 B1211 5 HET SO4 B1212 5 HET ACT B1213 4 HET ZT2 B1214 23 HET ZT2 B1215 23 HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM ZT2 5-[(E)-(2-OXO-2,3-DIHYDRO-1H-INDEN-1-YLIDENE)METHYL]-1, HETNAM 2 ZT2 3-BENZODIOXOLE-4-CARBOXYLIC ACID FORMUL 3 SO4 6(O4 S 2-) FORMUL 6 ACT 4(C2 H3 O2 1-) FORMUL 9 ZT2 4(C18 H12 O5) FORMUL 17 HOH *126(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 THR B 93 TRP B 108 1 16 HELIX 9 9 ASN B 117 SER B 123 1 7 HELIX 10 10 SER B 123 GLY B 134 1 12 HELIX 11 11 PRO B 145 ARG B 166 1 22 HELIX 12 12 ASP B 167 ALA B 169 5 3 HELIX 13 13 HIS B 171 LYS B 186 1 16 HELIX 14 14 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 SITE 1 AC1 6 THR A 66 HIS A 67 LYS A 111 LYS A 136 SITE 2 AC1 6 LYS A 159 HOH A2049 SITE 1 AC2 6 LYS A 71 ARG A 166 HIS A 171 LEU A 172 SITE 2 AC2 6 HOH A2009 HOH A2056 SITE 1 AC3 7 GLY A 94 SER A 123 THR A 124 THR A 125 SITE 2 AC3 7 HOH A2024 HOH A2026 HOH A2044 SITE 1 AC4 7 TYR A 99 LYS A 103 ACT A1214 HOH A2029 SITE 2 AC4 7 HOH A2068 GLU B 87 HOH B2051 SITE 1 AC5 7 GLU A 87 ACT A1213 HOH A2015 HOH A2017 SITE 2 AC5 7 HOH A2058 TYR B 99 LYS B 103 SITE 1 AC6 7 GLU A 85 GLU A 87 PHE A 100 LYS A 103 SITE 2 AC6 7 LEU A 104 ARG A 107 ARG B 107 SITE 1 AC7 9 GLN A 168 ALA A 169 GLU A 170 HIS A 171 SITE 2 AC7 9 THR A 174 MET A 178 GLN B 95 TYR B 99 SITE 3 AC7 9 ALA B 129 SITE 1 AC8 12 HIS A 185 ARG A 187 SER A 195 GLY A 197 SITE 2 AC8 12 GLU A 198 VAL A 201 HOH A2064 GLY B 106 SITE 3 AC8 12 ARG B 107 PRO B 109 ILE B 204 ILE B 208 SITE 1 AC9 6 THR B 66 HIS B 67 LYS B 111 LYS B 136 SITE 2 AC9 6 LYS B 159 HOH B2039 SITE 1 BC1 5 LYS B 71 ARG B 166 HIS B 171 LEU B 172 SITE 2 BC1 5 HOH B2050 SITE 1 BC2 6 GLY B 94 SER B 123 THR B 124 THR B 125 SITE 2 BC2 6 HOH B2021 HOH B2034 SITE 1 BC3 5 ARG A 107 GLU B 85 GLU B 87 PHE B 100 SITE 2 BC3 5 LYS B 103 SITE 1 BC4 11 GLN A 95 TYR A 99 ALA A 129 TRP A 132 SITE 2 BC4 11 GLN B 168 ALA B 169 GLU B 170 HIS B 171 SITE 3 BC4 11 THR B 174 MET B 178 HOH B2058 SITE 1 BC5 10 ARG A 107 PRO A 109 ILE A 204 ILE A 208 SITE 2 BC5 10 HIS B 185 ARG B 187 SER B 195 GLY B 197 SITE 3 BC5 10 GLU B 198 VAL B 201 CRYST1 71.331 71.331 66.979 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 0.014019 0.008094 0.000000 0.00000 SCALE2 0.000000 0.016188 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014930 0.00000