HEADER VIRAL PROTEIN/INHIBITOR 19-DEC-13 4O55 TITLE HIV-1 INTEGRASE CATALYTIC CORE DOMAIN COMPLEXED WITH ALLOSTERIC TITLE 2 INHIBITOR (2S)-TERT-BUTOXY[6-(5-CHLORO-1H-BENZIMIDAZOL-2-YL)-2,5- TITLE 3 DIMETHYL-4-PHENYLPYRIDIN-3-YL]ETHANOIC ACID CAVEAT 4O55 THE BOND LENGTH C CAF A 65 - N THR A 66 AND C ALA A 129 - N CAVEAT 2 4O55 CAF A 130 IS OUTSIDE ACCEPTED RANGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11698; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HIV INTEGRASE, CCD, DDE MOTIF, ALLOSTERIC INHIBITOR, VIRAL PROTEIN- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.FENG,M.KVARATSKHELIA REVDAT 2 22-NOV-17 4O55 1 REMARK REVDAT 1 02-JUL-14 4O55 0 JRNL AUTH A.SHARMA,A.SLAUGHTER,N.JENA,L.FENG,J.J.KESSL,H.J.FADEL, JRNL AUTH 2 N.MALANI,F.MALE,L.WU,E.POESCHLA,F.D.BUSHMAN,J.R.FUCHS, JRNL AUTH 3 M.KVARATSKHELIA JRNL TITL A NEW CLASS OF MULTIMERIZATION SELECTIVE INHIBITORS OF HIV-1 JRNL TITL 2 INTEGRASE. JRNL REF PLOS PATHOG. V. 10 04171 2014 JRNL REFN ISSN 1553-7366 JRNL PMID 24874515 JRNL DOI 10.1371/JOURNAL.PPAT.1004171 REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.12 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 9694 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 461 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) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 665 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 36 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1092 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.98000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : -3.19000 REMARK 3 B12 (A**2) : 0.49000 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): 0.205 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1158 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1562 ; 1.809 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 134 ; 6.438 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;32.121 ;24.783 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 190 ;20.841 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;13.466 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 175 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 827 ; 0.007 ; 0.020 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): 557 ; 2.781 ; 3.867 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 684 ; 4.043 ; 5.782 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 601 ; 4.749 ; 4.497 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 56 A 135 REMARK 3 ORIGIN FOR THE GROUP (A): -27.0679 26.6532 -17.1651 REMARK 3 T TENSOR REMARK 3 T11: 0.0924 T22: 0.1338 REMARK 3 T33: 0.0837 T12: -0.0066 REMARK 3 T13: 0.0257 T23: 0.0430 REMARK 3 L TENSOR REMARK 3 L11: 3.2475 L22: 1.6000 REMARK 3 L33: 4.4098 L12: 1.1746 REMARK 3 L13: 0.4168 L23: 0.9864 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.3579 S13: -0.0180 REMARK 3 S21: 0.0140 S22: -0.1291 S23: 0.1706 REMARK 3 S31: 0.2037 S32: -0.2881 S33: 0.1482 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 136 A 158 REMARK 3 ORIGIN FOR THE GROUP (A): -25.5329 22.1320 -8.4410 REMARK 3 T TENSOR REMARK 3 T11: 1.4176 T22: 1.0943 REMARK 3 T33: 0.7836 T12: -0.0343 REMARK 3 T13: 0.0104 T23: 0.4615 REMARK 3 L TENSOR REMARK 3 L11: 8.3698 L22: 8.7373 REMARK 3 L33: 8.4107 L12: 4.0670 REMARK 3 L13: 5.7206 L23: -2.5998 REMARK 3 S TENSOR REMARK 3 S11: 1.9628 S12: -1.4314 S13: -1.2508 REMARK 3 S21: 1.4872 S22: -0.2053 S23: 0.6788 REMARK 3 S31: 1.3091 S32: -1.0571 S33: -1.7575 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 159 A 209 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5233 27.9959 -11.2808 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.2422 REMARK 3 T33: 0.1041 T12: 0.0299 REMARK 3 T13: -0.0099 T23: 0.0701 REMARK 3 L TENSOR REMARK 3 L11: 3.9689 L22: 11.5929 REMARK 3 L33: 5.0034 L12: -0.4619 REMARK 3 L13: 0.0654 L23: 2.2498 REMARK 3 S TENSOR REMARK 3 S11: -0.0468 S12: -0.3995 S13: -0.3192 REMARK 3 S21: 0.5416 S22: 0.0960 S23: -0.7092 REMARK 3 S31: 0.4847 S32: 0.4175 S33: -0.0492 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: NULL REMARK 4 REMARK 4 4O55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10287 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 62.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6000 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) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.58400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.2.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG8000, 0.1 M NA CACODYLATE, PH REMARK 280 6.5, 0.1 M AMMONIUM SULPHATE, VAPOR DIFFUSION,HANGING DROP, REMARK 280 TEMPERATURE 277.5K, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 21.98100 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 43.96200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.96200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.98100 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: 4530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -43.96200 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 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 ILE A 141 REMARK 465 PRO A 142 REMARK 465 TYR A 143 REMARK 465 ASN A 144 REMARK 465 PRO A 145 REMARK 465 GLN A 146 REMARK 465 SER A 147 REMARK 465 GLN A 148 REMARK 465 GLY A 149 REMARK 465 VAL A 150 REMARK 465 ILE A 151 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 CAF A 65 CE2 REMARK 470 CAF A 130 CE2 REMARK 470 LYS A 188 CG CD CE NZ 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 ASP A 64 C CAF A 65 N 0.171 REMARK 500 CAF A 65 C THR A 66 N 0.275 REMARK 500 CAF A 130 C TRP A 131 N 0.232 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 ASP A 64 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 CAF A 65 O - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS A 188 57.88 -98.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 64 -11.40 REMARK 500 CAF A 65 25.75 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 LF9 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ITG RELATED DB: PDB REMARK 900 HIV-1 INTEGRASE CATALYTIC CORE DOMAIN REMARK 900 RELATED ID: 4O0J RELATED DB: PDB REMARK 900 RELATED ID: 4O5B RELATED DB: PDB DBREF 4O55 A 50 212 UNP P12497 POL_HV1N5 1197 1359 SEQADV 4O55 LYS A 185 UNP P12497 PHE 1332 CONFLICT SEQRES 1 A 163 MET HIS GLY GLN VAL ASP CYS SER PRO GLY ILE TRP GLN SEQRES 2 A 163 LEU ASP CAF THR HIS LEU GLU GLY LYS VAL ILE LEU VAL SEQRES 3 A 163 ALA VAL HIS VAL ALA SER GLY TYR ILE GLU ALA GLU VAL SEQRES 4 A 163 ILE PRO ALA GLU THR GLY GLN GLU THR ALA TYR PHE LEU SEQRES 5 A 163 LEU LYS LEU ALA GLY ARG TRP PRO VAL LYS THR VAL HIS SEQRES 6 A 163 THR ASP ASN GLY SER ASN PHE THR SER THR THR VAL LYS SEQRES 7 A 163 ALA ALA CAF TRP TRP ALA GLY ILE LYS GLN GLU PHE GLY SEQRES 8 A 163 ILE PRO TYR ASN PRO GLN SER GLN GLY VAL ILE GLU SER SEQRES 9 A 163 MET ASN LYS GLU LEU LYS LYS ILE ILE GLY GLN VAL ARG SEQRES 10 A 163 ASP GLN ALA GLU HIS LEU LYS THR ALA VAL GLN MET ALA SEQRES 11 A 163 VAL PHE ILE HIS ASN LYS LYS ARG LYS GLY GLY ILE GLY SEQRES 12 A 163 GLY TYR SER ALA GLY GLU ARG ILE VAL ASP ILE ILE ALA SEQRES 13 A 163 THR ASP ILE GLN THR LYS GLU MODRES 4O55 CAF A 65 CYS S-DIMETHYLARSINOYL-CYSTEINE MODRES 4O55 CAF A 130 CYS S-DIMETHYLARSINOYL-CYSTEINE HET CAF A 65 9 HET CAF A 130 9 HET LF9 A 301 33 HET SO4 A 302 5 HET SO4 A 303 5 HET SO4 A 304 5 HETNAM CAF S-DIMETHYLARSINOYL-CYSTEINE HETNAM LF9 (2S)-TERT-BUTOXY[6-(5-CHLORO-1H-BENZIMIDAZOL-2-YL)-2,5- HETNAM 2 LF9 DIMETHYL-4-PHENYLPYRIDIN-3-YL]ETHANOIC ACID HETNAM SO4 SULFATE ION HETSYN CAF CYSTEIN-S-YL CACODYLATE FORMUL 1 CAF 2(C5 H12 AS N O3 S) FORMUL 2 LF9 C26 H26 CL N3 O3 FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *42(H2 O) HELIX 1 1 THR A 93 GLY A 106 1 14 HELIX 2 2 ASN A 117 THR A 122 5 6 HELIX 3 3 SER A 123 GLY A 134 1 12 HELIX 4 4 SER A 153 ARG A 166 1 14 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 SHEET 1 A 5 ILE A 84 ILE A 89 0 SHEET 2 A 5 LYS A 71 HIS A 78 -1 N LEU A 74 O GLU A 87 SHEET 3 A 5 ILE A 60 LEU A 68 -1 N ASP A 64 O VAL A 75 SHEET 4 A 5 THR A 112 HIS A 114 1 O HIS A 114 N TRP A 61 SHEET 5 A 5 LYS A 136 GLU A 138 1 O GLU A 138 N VAL A 113 LINK C ASP A 64 N CAF A 65 1555 1555 1.51 LINK C CAF A 65 N THR A 66 1555 1555 1.61 LINK C ALA A 129 N CAF A 130 1555 1555 1.68 LINK C CAF A 130 N TRP A 131 1555 1555 1.57 CISPEP 1 GLU A 152 SER A 153 0 16.73 SITE 1 AC1 11 GLN A 95 THR A 124 THR A 125 ALA A 128 SITE 2 AC1 11 ALA A 129 ALA A 169 GLU A 170 HIS A 171 SITE 3 AC1 11 THR A 174 MET A 178 HOH A 424 SITE 1 AC2 8 GLY A 94 GLN A 95 SER A 123 THR A 124 SITE 2 AC2 8 THR A 125 HOH A 413 HOH A 417 HOH A 428 SITE 1 AC3 5 LYS A 71 HIS A 171 LEU A 172 HOH A 418 SITE 2 AC3 5 HOH A 433 SITE 1 AC4 3 THR A 66 HIS A 67 LYS A 159 CRYST1 71.730 71.730 65.943 90.00 90.00 120.00 P 31 2 1 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 0.013941 0.008049 0.000000 0.00000 SCALE2 0.000000 0.016098 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015165 0.00000