HEADER HYDROLASE/HYDROLASE INHIBITOR 09-JUN-10 3NF7 TITLE STRUCTURAL BASIS FOR A NEW MECHANISM OF INHIBITION OF HIV INTEGRASE TITLE 2 IDENTIFIED BY FRAGMENT SCREENING AND STRUCTURE BASED DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, UNP RESIDUES 50-212; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTEGRASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.NEWMAN,J.J.DEADMAN,D.RHODES REVDAT 3 20-MAR-24 3NF7 1 REMARK SEQADV REVDAT 2 02-MAY-12 3NF7 1 JRNL VERSN REVDAT 1 27-APR-11 3NF7 0 JRNL AUTH D.I.RHODES,T.S.PEAT,N.VANDEGRAAFF,D.JEEVARAJAH,G.LE, JRNL AUTH 2 E.D.JONES,J.A.SMITH,J.A.COATES,L.J.WINFIELD,N.THIENTHONG, JRNL AUTH 3 J.NEWMAN,D.LUCENT,J.H.RYAN,G.P.SAVAGE,C.L.FRANCIS, JRNL AUTH 4 J.J.DEADMAN JRNL TITL STRUCTURAL BASIS FOR A NEW MECHANISM OF INHIBITION OF HIV-1 JRNL TITL 2 INTEGRASE IDENTIFIED BY FRAGMENT SCREENING AND JRNL TITL 3 STRUCTURE-BASED DESIGN JRNL REF ANTIVIR.CHEM.CHEMOTHER. V. 21 155 2011 JRNL REFN ISSN 0956-3202 JRNL PMID 21602613 JRNL DOI 10.3851/IMP1716 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33527 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1768 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2510 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.2580 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 : 134 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2696 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3699 ; 2.402 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 5.902 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 111 ;34.562 ;25.315 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 462 ;15.244 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.807 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.202 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2090 ; 0.013 ; 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): 1610 ; 1.644 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2622 ; 2.746 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1086 ; 3.698 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1060 ; 5.425 ; 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 3NF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 66.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 ACETATE PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 22.30500 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 44.61000 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 300 REMARK: AT LEAST A DIMER IF NOT A TETRAMER IN THE CELL; SEEN AS A REMARK 300 DIMER IN SOLUTION AND IN THE CRYSTAL 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: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 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 30 REMARK 465 GLY A 31 REMARK 465 SER A 32 REMARK 465 SER A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 HIS A 36 REMARK 465 HIS A 37 REMARK 465 HIS A 38 REMARK 465 HIS A 39 REMARK 465 SER A 40 REMARK 465 SER A 41 REMARK 465 GLY A 42 REMARK 465 LEU A 43 REMARK 465 VAL A 44 REMARK 465 PRO A 45 REMARK 465 ARG A 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 HIS A 49 REMARK 465 MET A 50 REMARK 465 HIS A 51 REMARK 465 GLY A 52 REMARK 465 GLN A 53 REMARK 465 VAL A 54 REMARK 465 ASP 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 30 REMARK 465 GLY B 31 REMARK 465 SER B 32 REMARK 465 SER B 33 REMARK 465 HIS B 34 REMARK 465 HIS B 35 REMARK 465 HIS B 36 REMARK 465 HIS B 37 REMARK 465 HIS B 38 REMARK 465 HIS B 39 REMARK 465 SER B 40 REMARK 465 SER B 41 REMARK 465 GLY B 42 REMARK 465 LEU B 43 REMARK 465 VAL B 44 REMARK 465 PRO B 45 REMARK 465 ARG B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 HIS B 49 REMARK 465 MET B 50 REMARK 465 HIS B 51 REMARK 465 GLY B 52 REMARK 465 GLN B 53 REMARK 465 VAL B 54 REMARK 465 ASP 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 O3 SO4 A 7 O2 EDO B 214 1.83 REMARK 500 N SER A 57 O HOH A 284 1.87 REMARK 500 O HOH A 284 O HOH A 286 1.93 REMARK 500 OE1 GLU A 87 OXT ACY B 5 2.01 REMARK 500 OD1 ASP B 139 O HOH B 283 2.03 REMARK 500 OE1 GLU B 87 O ACY A 215 2.04 REMARK 500 O HOH A 220 O HOH B 287 2.05 REMARK 500 N SER B 57 O HOH B 242 2.19 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 GLU A 87 CG GLU A 87 CD 0.102 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 116 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 PHE B 100 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES 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 A 146 0.74 -66.79 REMARK 500 PRO B 142 70.59 -68.87 REMARK 500 PRO B 142 70.59 -67.37 REMARK 500 GLN B 146 -5.04 -59.83 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 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 9 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIW A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 10 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIW B 215 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BHL RELATED DB: PDB REMARK 900 CACODYLATED CATALYTIC DOMAIN OF HIV-1 INTEGRASE REMARK 900 RELATED ID: 1BI4 RELATED DB: PDB REMARK 900 CATALYTIC DOMAIN OF HIV-1 INTEGRASE REMARK 900 RELATED ID: 1BIU RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE CORE DOMAIN COMPLEXED WITH MG++ REMARK 900 RELATED ID: 1EX4 RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE CATALYTIC CORE AND C-TERMINAL DOMAIN REMARK 900 RELATED ID: 1K6Y RELATED DB: PDB REMARK 900 TWO-DOMAIN FRAGMENT OF HIV-1 INTEGRASE REMARK 900 RELATED ID: 3NF6 RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, DIFFERENT INHIBITOR REMARK 900 RELATED ID: 3NF8 RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, DIFFERENT INHIBITOR REMARK 900 RELATED ID: 3NF9 RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, DIFFERENT INHIBITOR REMARK 900 RELATED ID: 3NFA RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE, DIFFERENT INHIBITOR DBREF 3NF7 A 50 212 UNP Q76353 Q76353_9HIV1 50 212 DBREF 3NF7 B 50 212 UNP Q76353 Q76353_9HIV1 50 212 SEQADV 3NF7 MET A 30 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY A 31 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 32 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 33 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 34 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 35 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 36 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 37 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 38 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 39 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 40 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 41 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY A 42 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 LEU A 43 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 VAL A 44 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 PRO A 45 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 ARG A 46 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY A 47 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 48 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS A 49 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER A 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3NF7 ASP A 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3NF7 HIS A 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQADV 3NF7 MET B 30 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY B 31 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 32 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 33 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 34 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 35 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 36 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 37 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 38 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 39 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 40 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 41 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY B 42 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 LEU B 43 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 VAL B 44 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 PRO B 45 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 ARG B 46 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 GLY B 47 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 48 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 HIS B 49 UNP Q76353 EXPRESSION TAG SEQADV 3NF7 SER B 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 3NF7 ASP B 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 3NF7 HIS B 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQRES 1 A 183 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 183 LEU VAL PRO ARG GLY SER HIS MET HIS GLY GLN VAL ASP SEQRES 3 A 183 SER SER PRO GLY ILE TRP GLN LEU ASP CYS THR HIS LEU SEQRES 4 A 183 GLU GLY LYS VAL ILE LEU VAL ALA VAL HIS VAL ALA SER SEQRES 5 A 183 GLY TYR ILE GLU ALA GLU VAL ILE PRO ALA GLU THR GLY SEQRES 6 A 183 GLN GLU THR ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG SEQRES 7 A 183 TRP PRO VAL LYS THR VAL HIS THR ASP ASN GLY SER ASN SEQRES 8 A 183 PHE THR SER THR THR VAL LYS ALA ALA CYS TRP TRP ALA SEQRES 9 A 183 GLY ILE LYS GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SEQRES 10 A 183 SER GLN GLY VAL ILE GLU SER MET ASN LYS GLU LEU LYS SEQRES 11 A 183 LYS ILE ILE GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU SEQRES 12 A 183 LYS THR ALA VAL GLN MET ALA VAL PHE ILE HIS ASN HIS SEQRES 13 A 183 LYS ARG LYS GLY GLY ILE GLY GLY TYR SER ALA GLY GLU SEQRES 14 A 183 ARG ILE VAL ASP ILE ILE ALA THR ASP ILE GLN THR LYS SEQRES 15 A 183 GLU SEQRES 1 B 183 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 183 LEU VAL PRO ARG GLY SER HIS MET HIS GLY GLN VAL ASP SEQRES 3 B 183 SER SER PRO GLY ILE TRP GLN LEU ASP CYS THR HIS LEU SEQRES 4 B 183 GLU GLY LYS VAL ILE LEU VAL ALA VAL HIS VAL ALA SER SEQRES 5 B 183 GLY TYR ILE GLU ALA GLU VAL ILE PRO ALA GLU THR GLY SEQRES 6 B 183 GLN GLU THR ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG SEQRES 7 B 183 TRP PRO VAL LYS THR VAL HIS THR ASP ASN GLY SER ASN SEQRES 8 B 183 PHE THR SER THR THR VAL LYS ALA ALA CYS TRP TRP ALA SEQRES 9 B 183 GLY ILE LYS GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SEQRES 10 B 183 SER GLN GLY VAL ILE GLU SER MET ASN LYS GLU LEU LYS SEQRES 11 B 183 LYS ILE ILE GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU SEQRES 12 B 183 LYS THR ALA VAL GLN MET ALA VAL PHE ILE HIS ASN HIS SEQRES 13 B 183 LYS ARG LYS GLY GLY ILE GLY GLY TYR SER ALA GLY GLU SEQRES 14 B 183 ARG ILE VAL ASP ILE ILE ALA THR ASP ILE GLN THR LYS SEQRES 15 B 183 GLU HET SO4 A 2 5 HET SO4 A 4 5 HET SO4 A 5 5 HET SO4 A 7 5 HET SO4 A 9 5 HET ACY A 1 4 HET ACY A 213 4 HET ACY A 214 4 HET ACY A 215 4 HET ACY A 8 4 HET EDO A 216 4 HET CIW A 221 24 HET SO4 B 1 5 HET SO4 B 3 5 HET SO4 B 6 5 HET SO4 B 8 5 HET SO4 B 10 5 HET ACY B 213 4 HET ACY B 5 4 HET EDO B 214 4 HET CIW B 215 24 HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM CIW 5-[(5-CHLORO-2-OXO-2,3-DIHYDRO-1H-INDOL-1-YL)METHYL]-1, HETNAM 2 CIW 3-BENZODIOXOLE-4-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 10(O4 S 2-) FORMUL 8 ACY 7(C2 H4 O2) FORMUL 13 EDO 2(C2 H6 O2) FORMUL 14 CIW 2(C17 H12 CL N O5) FORMUL 24 HOH *169(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 A 5 ILE A 84 ILE A 89 0 SHEET 2 A 5 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 A 5 ILE A 60 LEU A 68 -1 N THR A 66 O ILE A 73 SHEET 4 A 5 THR A 112 HIS A 114 1 O HIS A 114 N LEU A 63 SHEET 5 A 5 LYS A 136 GLU A 138 1 O GLU A 138 N VAL A 113 SHEET 1 B 5 ILE B 84 ILE B 89 0 SHEET 2 B 5 LYS B 71 HIS B 78 -1 N ALA B 76 O GLU B 85 SHEET 3 B 5 ILE B 60 LEU B 68 -1 N THR B 66 O ILE B 73 SHEET 4 B 5 THR B 112 HIS B 114 1 O HIS B 114 N LEU B 63 SHEET 5 B 5 LYS B 136 GLU B 138 1 O GLU B 138 N VAL B 113 SITE 1 AC1 7 HOH A 26 THR A 66 HIS A 67 LYS A 111 SITE 2 AC1 7 LYS A 136 LYS A 159 HOH A 273 SITE 1 AC2 4 LYS A 71 HIS A 171 LEU A 172 HOH A 222 SITE 1 AC3 6 GLY A 94 SER A 123 THR A 124 THR A 125 SITE 2 AC3 6 HOH A 251 HOH A 275 SITE 1 AC4 6 ALA A 169 GLU A 170 HIS A 171 THR A 174 SITE 2 AC4 6 HOH A 279 EDO B 214 SITE 1 AC5 6 GLU A 85 ALA A 86 GLU A 87 PHE A 100 SITE 2 AC5 6 LYS A 103 ARG B 107 SITE 1 AC6 5 THR A 174 MET A 178 ALA B 128 ALA B 129 SITE 2 AC6 5 TRP B 132 SITE 1 AC7 6 ALA A 128 ALA A 129 TRP A 132 HOH A 277 SITE 2 AC7 6 THR B 174 MET B 178 SITE 1 AC8 8 ALA A 105 GLY A 106 ARG A 107 TRP A 108 SITE 2 AC8 8 TYR B 83 ASN B 184 HIS B 185 GLY B 197 SITE 1 AC9 7 TYR A 99 LYS A 103 HOH A 237 ACY B 5 SITE 2 AC9 7 HOH B 15 GLU B 87 HOH B 238 SITE 1 BC1 5 HIS A 67 VAL A 72 ALA A 91 GLU A 92 SITE 2 BC1 5 HOH A 290 SITE 1 BC2 6 GLN A 95 HOH A 252 HOH A 282 HOH A 285 SITE 2 BC2 6 SO4 B 8 HOH B 276 SITE 1 BC3 11 VAL A 79 GLY A 82 ILE A 84 VAL A 150 SITE 2 BC3 11 ILE A 151 SER A 153 MET A 154 GLU A 157 SITE 3 BC3 11 LEU A 158 HIS A 183 HOH A 272 SITE 1 BC4 7 HOH B 22 THR B 66 HIS B 67 LYS B 111 SITE 2 BC4 7 LYS B 136 LYS B 159 HOH B 285 SITE 1 BC5 4 LYS B 71 HIS B 171 LEU B 172 HOH B 219 SITE 1 BC6 6 GLY B 94 SER B 123 THR B 124 THR B 125 SITE 2 BC6 6 HOH B 257 HOH B 266 SITE 1 BC7 7 EDO A 216 HOH A 277 ALA B 169 GLU B 170 SITE 2 BC7 7 HIS B 171 THR B 174 HOH B 276 SITE 1 BC8 6 ARG A 107 GLU B 85 ALA B 86 GLU B 87 SITE 2 BC8 6 PHE B 100 LYS B 103 SITE 1 BC9 8 TYR A 83 ASN A 184 HIS A 185 GLY A 197 SITE 2 BC9 8 ALA B 105 GLY B 106 ARG B 107 TRP B 108 SITE 1 CC1 7 HOH A 16 GLU A 87 ACY A 215 HOH A 246 SITE 2 CC1 7 TYR B 99 LYS B 103 HOH B 231 SITE 1 CC2 7 SO4 A 7 THR A 174 HOH A 279 GLN B 95 SITE 2 CC2 7 TYR B 99 HOH B 246 HOH B 258 SITE 1 CC3 10 GLN B 62 VAL B 79 GLY B 82 ILE B 84 SITE 2 CC3 10 VAL B 150 ILE B 151 MET B 154 GLU B 157 SITE 3 CC3 10 LEU B 158 HIS B 183 CRYST1 71.333 71.333 66.915 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 0.016187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014944 0.00000