PDB Short entry for 3AVK HEADER RECOMBINATION/INHIBITOR 05-MAR-11 3AVK TITLE CRYSTAL STRUCTURES OF NOVEL ALLOSTERIC PEPTIDE INHIBITORS OF HIV TITLE 2 INTEGRASE IN THE LEDGF BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CCD DOMAIN (UNP RESIDUES 1197-1359); COMPND 5 SYNONYM: IN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LEDGF PEPTIDE; COMPND 10 CHAIN: D, F; COMPND 11 SYNONYM: LENS EPITHELIAL DERIVED GROWTH FACTOR PEPTIDE; COMPND 12 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 STRAIN: NEW YORK-5 ISOLATE; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 OTHER_DETAILS: CHEMICAL SYNTHSIS KEYWDS PROTEIN-PROTEIN INTERACTIONS, HIV, RECOMBINATION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.S.PEAT,J.J.DEADMAN,J.NEWMAN,D.I.RHODES REVDAT 2 19-JUN-13 3AVK 1 JRNL REVDAT 1 18-JAN-12 3AVK 0 JRNL AUTH D.I.RHODES,T.S.PEAT,N.VANDEGRAAFF,D.JEEVARAJAH,J.NEWMAN, JRNL AUTH 2 J.MARTYN,J.A.COATES,N.J.EDE,P.REA,J.J.DEADMAN JRNL TITL CRYSTAL STRUCTURES OF NOVEL ALLOSTERIC PEPTIDE INHIBITORS OF JRNL TITL 2 HIV INTEGRASE IDENTIFY NEW INTERACTIONS AT THE LEDGF BINDING JRNL TITL 3 SITE. JRNL REF CHEMBIOCHEM V. 12 2311 2011 JRNL REFN ISSN 1439-4227 JRNL PMID 21850718 JRNL DOI 10.1002/CBIC.201100350 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0062 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 37630 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1880 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2678 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2446 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.10000 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): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.751 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2767 ; 0.030 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3798 ; 2.318 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 366 ; 6.309 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;29.933 ;25.763 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 496 ;14.552 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;10.671 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 431 ; 0.198 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2086 ; 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): 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3AVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAR-11. REMARK 100 THE RCSB ID CODE IS RCSB029748. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 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 : 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 : 37635 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 61.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40MM TRIS PH 8.0, 250MM NACL, 30MM REMARK 280 MGCL2, 5MM DTT, 1.6-2.0M AMMONIUM SULFATE, 100MM SODIUM ACETATE REMARK 280 BUFFER PH 5.0-5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K, VAPOR DIFFUSION, SITTING DROP 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 22.20300 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 44.40600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, F 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 REMARK 400 THE SLKIDNED PEPTIDE IS CYCLIC PEPTIDE, A MEMBER OF ENZYME REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: SLKIDNED PEPTIDE REMARK 400 CHAIN: D, F REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 OE1 GLU A 87 O HOH A 229 1.67 REMARK 500 OE1 GLU B 87 O HOH B 240 1.78 REMARK 500 O HOH A 221 O HOH B 264 1.98 REMARK 500 O HOH A 238 O HOH A 270 2.03 REMARK 500 O HOH B 256 O HOH B 265 2.05 REMARK 500 O HOH A 227 O HOH B 269 2.05 REMARK 500 O HOH B 251 O HOH B 262 2.08 REMARK 500 O HOH A 239 O HOH A 258 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 228 OE2 GLU B 152 2665 2.09 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 LEU A 74 CB - CG - CD2 ANGL. DEV. = -10.2 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 ASN D 6 84.11 -168.98 REMARK 500 ASN F 6 85.52 -165.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 SER B 57 24.6 L L OUTSIDE RANGE 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 ACY A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF LEDGF PEPTIDE REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN F OF LEDGF PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AV9 RELATED DB: PDB REMARK 900 RELATED ID: 3AVA RELATED DB: PDB REMARK 900 RELATED ID: 3AVB RELATED DB: PDB REMARK 900 RELATED ID: 3AVC RELATED DB: PDB REMARK 900 RELATED ID: 3AVF RELATED DB: PDB REMARK 900 RELATED ID: 3AVG RELATED DB: PDB REMARK 900 RELATED ID: 3AVH RELATED DB: PDB REMARK 900 RELATED ID: 3AVI RELATED DB: PDB REMARK 900 RELATED ID: 3AVJ RELATED DB: PDB REMARK 900 RELATED ID: 3AVL RELATED DB: PDB REMARK 900 RELATED ID: 3AVM RELATED DB: PDB REMARK 900 RELATED ID: 3AVN RELATED DB: PDB DBREF 3AVK A 50 212 UNP P12497 POL_HV1N5 1197 1359 DBREF 3AVK B 50 212 UNP P12497 POL_HV1N5 1197 1359 DBREF 3AVK D 1 8 PDB 3AVK 3AVK 1 8 DBREF 3AVK F 1 8 PDB 3AVK 3AVK 1 8 SEQADV 3AVK MET A 30 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY A 31 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 32 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 33 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 34 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 35 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 36 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 37 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 38 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 39 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 40 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 41 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY A 42 UNP P12497 EXPRESSION TAG SEQADV 3AVK LEU A 43 UNP P12497 EXPRESSION TAG SEQADV 3AVK VAL A 44 UNP P12497 EXPRESSION TAG SEQADV 3AVK PRO A 45 UNP P12497 EXPRESSION TAG SEQADV 3AVK ARG A 46 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY A 47 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 48 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS A 49 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER A 56 UNP P12497 CYS 1203 ENGINEERED MUTATION SEQADV 3AVK ASP A 139 UNP P12497 PHE 1286 ENGINEERED MUTATION SEQADV 3AVK HIS A 185 UNP P12497 PHE 1332 ENGINEERED MUTATION SEQADV 3AVK MET B 30 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY B 31 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 32 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 33 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 34 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 35 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 36 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 37 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 38 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 39 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 40 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 41 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY B 42 UNP P12497 EXPRESSION TAG SEQADV 3AVK LEU B 43 UNP P12497 EXPRESSION TAG SEQADV 3AVK VAL B 44 UNP P12497 EXPRESSION TAG SEQADV 3AVK PRO B 45 UNP P12497 EXPRESSION TAG SEQADV 3AVK ARG B 46 UNP P12497 EXPRESSION TAG SEQADV 3AVK GLY B 47 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 48 UNP P12497 EXPRESSION TAG SEQADV 3AVK HIS B 49 UNP P12497 EXPRESSION TAG SEQADV 3AVK SER B 56 UNP P12497 CYS 1203 ENGINEERED MUTATION SEQADV 3AVK ASP B 139 UNP P12497 PHE 1286 ENGINEERED MUTATION SEQADV 3AVK HIS B 185 UNP P12497 PHE 1332 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 SEQRES 1 D 8 SER LEU LYS ILE ASP ASN GLU ASP SEQRES 1 F 8 SER LEU LYS ILE ASP ASN GLU ASP HET SO4 A 2 5 HET SO4 A 4 5 HET SO4 A 5 5 HET SO4 A 7 5 HET ACY A 1 4 HET CL A 213 1 HET SO4 B 1 5 HET SO4 B 3 5 HET SO4 B 6 5 HET SO4 B 8 5 HET ACY B 2 4 HET CL B 213 1 HETNAM SO4 SULFATE ION HETNAM ACY ACETIC ACID HETNAM CL CHLORIDE ION FORMUL 5 SO4 8(O4 S 2-) FORMUL 9 ACY 2(C2 H4 O2) FORMUL 10 CL 2(CL 1-) FORMUL 17 HOH *141(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 ALA A 133 1 11 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 ALA B 133 1 11 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 VAL A 72 O ILE A 89 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 VAL B 72 O ILE B 89 SHEET 3 B 5 ILE B 60 LEU B 68 -1 N GLN B 62 O VAL B 77 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 LINK C ASP D 8 N SER D 1 1555 1555 1.34 LINK C ASP F 8 N SER F 1 1555 1555 1.34 SITE 1 AC1 7 THR A 66 HIS A 67 LYS A 111 LYS A 136 SITE 2 AC1 7 LYS A 159 HOH A 220 HOH A 236 SITE 1 AC2 6 LYS A 71 ARG A 166 HIS A 171 LEU A 172 SITE 2 AC2 6 HOH A 222 HOH A 235 SITE 1 AC3 8 HOH A 19 GLY A 94 SER A 123 THR A 124 SITE 2 AC3 8 THR A 125 HOH A 218 HOH A 248 HOH D 126 SITE 1 AC4 9 GLU A 85 GLU A 87 PHE A 100 LYS A 103 SITE 2 AC4 9 ARG A 107 HOH A 243 SO4 B 8 LYS B 103 SITE 3 AC4 9 ARG B 107 SITE 1 AC5 6 ALA A 105 GLY A 106 TRP A 108 ASN B 184 SITE 2 AC5 6 HIS B 185 GLY B 197 SITE 1 AC6 2 VAL A 72 GLU A 92 SITE 1 AC7 6 THR B 66 HIS B 67 LYS B 111 LYS B 136 SITE 2 AC7 6 LYS B 159 HOH B 228 SITE 1 AC8 6 LYS B 71 ARG B 166 HIS B 171 LEU B 172 SITE 2 AC8 6 HOH B 234 HOH B 236 SITE 1 AC9 8 HOH B 26 GLY B 94 SER B 123 THR B 124 SITE 2 AC9 8 THR B 125 HOH B 217 HOH B 251 HOH F 127 SITE 1 BC1 7 SO4 A 7 ARG A 107 GLU B 85 ALA B 86 SITE 2 BC1 7 GLU B 87 PHE B 100 LYS B 103 SITE 1 BC2 6 ASN A 184 HIS A 185 GLY A 197 ALA B 105 SITE 2 BC2 6 GLY B 106 TRP B 108 SITE 1 BC3 2 VAL B 72 GLU B 92 SITE 1 BC4 14 GLN A 95 THR A 125 ALA A 128 TRP A 131 SITE 2 BC4 14 ILE A 141 TYR A 143 ASP B 167 GLN B 168 SITE 3 BC4 14 ALA B 169 GLU B 170 HIS B 171 THR B 174 SITE 4 BC4 14 MET B 178 HOH D 126 SITE 1 BC5 14 ASP A 167 GLN A 168 ALA A 169 GLU A 170 SITE 2 BC5 14 HIS A 171 THR A 174 HOH A 266 GLN B 95 SITE 3 BC5 14 THR B 125 ALA B 128 TRP B 131 ILE B 141 SITE 4 BC5 14 TYR B 143 HOH F 127 CRYST1 70.743 70.743 66.609 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 0.014136 0.008161 0.000000 0.00000 SCALE2 0.000000 0.016322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015013 0.00000