HEADER TRANSFERASE/TRANSFERASE BINDING PROTEIN 07-FEB-15 4Y1C TITLE CYCLIC HEXAPEPTIDE CYC[NDPOPPKID] IN COMPLEX WITH HIV-1 INTEGRASE CORE TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 50-212; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CYCLIC HEXAPEPTIDE CYC[NDPOPPKID]; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS DNA INTEGRATION, AIDS, ENDONUCLEASE, POLYNUCLEOTIDYL TRANSFERASE, DNA KEYWDS 2 BINDING, VIRAL PROTEIN, RNASEH, LEDGF, LENS EPITHELIUM DERIVED KEYWDS 3 GROWTH FACTOR, VIRAL PROTEIN-PEPTIDE COMPLEX, TRANSFERASE- KEYWDS 4 TRANSFERASE BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.WIELENS,D.K.CHALMERS REVDAT 3 27-SEP-23 4Y1C 1 REMARK LINK REVDAT 2 01-JUN-16 4Y1C 1 SOURCE REMARK REVDAT 1 25-FEB-15 4Y1C 0 JRNL AUTH S.E.NORTHFIELD,J.WIELENS,S.J.HEADEY,M.MULCAIR,M.J.SCANLON, JRNL AUTH 2 M.W.PARKER,P.E.THOMPSON,D.K.CHALMERS JRNL TITL HEXAPEPTIDE MIMETICS OF LEDGF IN COMPLEX WITH HIV-1 JRNL TITL 2 INTEGRASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 12462 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) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 656 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 611 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 68.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.4260 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.5750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : 1.93000 REMARK 3 B33 (A**2) : -1.38000 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): 0.483 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.302 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.198 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.836 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.875 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.835 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2296 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3108 ; 1.878 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 282 ; 6.777 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;34.796 ;25.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 392 ;19.333 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;10.803 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1684 ; 0.008 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4Y1C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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) : 0.95369 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 6.930 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.23 REMARK 200 R MERGE FOR SHELL (I) : 0.05300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.320 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3WNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.15M SODIUM REMARK 280 REMARK 280 CITRATE, 5MM CADMIUM CHLORIDE, PH 4.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 30.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.72000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.72000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 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 208 REMARK 465 GLN A 209 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 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 ASP B 139 REMARK 465 GLY B 140 REMARK 465 ILE B 141 REMARK 465 PRO B 142 REMARK 465 TYR B 143 REMARK 465 ASN B 144 REMARK 465 PRO B 145 REMARK 465 GLN B 146 REMARK 465 SER B 147 REMARK 465 GLN B 148 REMARK 465 GLY B 149 REMARK 465 VAL B 150 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 N LYS C 1 C PRO C 6 1.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 183 CG HIS A 183 CD2 0.060 REMARK 500 HIS B 185 CG HIS B 185 CD2 0.059 REMARK 500 LYS C 1 C DIL C 2 N 0.164 REMARK 500 DIL C 2 C ASP C 3 N 0.143 REMARK 500 ASN C 4 C 45F C 5 N 0.180 REMARK 500 45F C 5 C PRO C 6 N 0.166 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 ASN C 4 N - CA - CB ANGL. DEV. = 12.6 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 GLU B 69 27.15 47.23 REMARK 500 ASP B 116 -165.24 -63.29 REMARK 500 ILE B 208 13.73 -66.05 REMARK 500 ASP C 3 -16.95 139.26 REMARK 500 ASN C 4 80.76 -170.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 HIS A 67 NE2 115.2 REMARK 620 3 GLU A 92 OE1 101.5 98.5 REMARK 620 4 ASP B 131 O 62.2 58.4 86.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 GLU A 92 OE2 102.0 REMARK 620 3 ASP A 116 OD2 93.6 160.6 REMARK 620 4 ASP B 131 OD2 44.1 77.9 106.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1002 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 65 SG REMARK 620 2 HIS B 67 NE2 100.1 REMARK 620 3 GLU B 92 OE1 119.6 95.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B1001 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 92 OE2 REMARK 620 2 ASP B 116 OD2 161.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD 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 CD B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WNE RELATED DB: PDB REMARK 900 INTEGRASE CORE DOMAIN IN COMPLEX WITH A CIRCULAR PEPTIDE REMARK 900 RELATED ID: 3WNF RELATED DB: PDB REMARK 900 RELATED ID: 3WNG RELATED DB: PDB REMARK 900 RELATED ID: 3WNH RELATED DB: PDB REMARK 900 RELATED ID: 4Y1D RELATED DB: PDB DBREF 4Y1C A 50 212 UNP Q76353 Q76353_9HIV1 50 212 DBREF 4Y1C B 50 212 UNP Q76353 Q76353_9HIV1 50 212 DBREF 4Y1C C 1 6 PDB 4Y1C 4Y1C 1 6 SEQADV 4Y1C MET A 46 UNP Q76353 INITIATING METHIONINE SEQADV 4Y1C GLY A 47 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C SER A 48 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C HIS A 49 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C SER A 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 4Y1C ASP A 131 UNP Q76353 TRP 131 ENGINEERED MUTATION SEQADV 4Y1C ASP A 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 4Y1C HIS A 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQADV 4Y1C MET B 46 UNP Q76353 INITIATING METHIONINE SEQADV 4Y1C GLY B 47 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C SER B 48 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C HIS B 49 UNP Q76353 EXPRESSION TAG SEQADV 4Y1C SER B 56 UNP Q76353 CYS 56 ENGINEERED MUTATION SEQADV 4Y1C ASP B 131 UNP Q76353 TRP 131 ENGINEERED MUTATION SEQADV 4Y1C ASP B 139 UNP Q76353 PHE 139 ENGINEERED MUTATION SEQADV 4Y1C HIS B 185 UNP Q76353 PHE 185 ENGINEERED MUTATION SEQRES 1 A 167 MET GLY SER HIS MET HIS GLY GLN VAL ASP 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 ASP 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 HIS MET HIS GLY GLN VAL ASP 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 ASP 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 SEQRES 1 C 6 LYS DIL ASP ASN 45F PRO HET DIL C 2 8 HET 45F C 5 11 HET CD A 301 1 HET CD A 302 1 HET SO4 A 303 5 HET CD B1001 1 HET CD B1002 1 HET SO4 B1003 5 HETNAM DIL D-ISOLEUCINE HETNAM 45F (4S)-4-(PROP-2-YN-1-YLOXY)-L-PROLINE HETNAM CD CADMIUM ION HETNAM SO4 SULFATE ION FORMUL 3 DIL C6 H13 N O2 FORMUL 3 45F C8 H11 N O3 FORMUL 4 CD 4(CD 2+) FORMUL 6 SO4 2(O4 S 2-) FORMUL 10 HOH *24(H2 O) HELIX 1 AA1 THR A 93 TRP A 108 1 16 HELIX 2 AA2 GLY A 118 SER A 123 1 6 HELIX 3 AA3 SER A 123 ALA A 133 1 11 HELIX 4 AA4 GLU A 152 ARG A 166 1 15 HELIX 5 AA5 ASP A 167 ALA A 169 5 3 HELIX 6 AA6 HIS A 171 LYS A 186 1 16 HELIX 7 AA7 ALA A 196 ALA A 205 1 10 HELIX 8 AA8 THR B 93 TRP B 108 1 16 HELIX 9 AA9 GLY B 118 THR B 122 5 5 HELIX 10 AB1 SER B 123 GLY B 134 1 12 HELIX 11 AB2 ILE B 151 MET B 154 5 4 HELIX 12 AB3 ASN B 155 ARG B 166 1 12 HELIX 13 AB4 ASP B 167 ALA B 169 5 3 HELIX 14 AB5 HIS B 171 LYS B 186 1 16 HELIX 15 AB6 ALA B 196 ILE B 208 1 13 SHEET 1 AA1 5 ILE A 84 ILE A 89 0 SHEET 2 AA1 5 LYS A 71 HIS A 78 -1 N VAL A 72 O ILE A 89 SHEET 3 AA1 5 ILE A 60 LEU A 68 -1 N THR A 66 O ILE A 73 SHEET 4 AA1 5 THR A 112 THR A 115 1 O HIS A 114 N LEU A 63 SHEET 5 AA1 5 LYS A 136 ASP A 139 1 O GLU A 138 N VAL A 113 SHEET 1 AA2 2 ARG A 187 LYS A 188 0 SHEET 2 AA2 2 TYR A 194 SER A 195 -1 O TYR A 194 N LYS A 188 SHEET 1 AA3 5 ILE B 84 ILE B 89 0 SHEET 2 AA3 5 LYS B 71 HIS B 78 -1 N ALA B 76 O GLU B 85 SHEET 3 AA3 5 ILE B 60 LEU B 68 -1 N THR B 66 O ILE B 73 SHEET 4 AA3 5 THR B 112 THR B 115 1 O HIS B 114 N LEU B 63 SHEET 5 AA3 5 LYS B 136 GLU B 138 1 O LYS B 136 N VAL B 113 SHEET 1 AA4 2 ARG B 187 LYS B 188 0 SHEET 2 AA4 2 TYR B 194 SER B 195 -1 O TYR B 194 N LYS B 188 LINK C LYS C 1 N DIL C 2 1555 1555 1.50 LINK C DIL C 2 N ASP C 3 1555 1555 1.48 LINK C ASN C 4 N 45F C 5 1555 1555 1.52 LINK C 45F C 5 N PRO C 6 1555 1555 1.50 LINK SG CYS A 65 CD CD A 301 1555 1555 2.59 LINK SG CYS A 65 CD CD A 302 1555 1555 2.60 LINK NE2 HIS A 67 CD CD A 301 1555 1555 2.32 LINK OE1 GLU A 92 CD CD A 301 1555 1555 1.86 LINK OE2 GLU A 92 CD CD A 302 1555 1555 2.37 LINK OD2 ASP A 116 CD CD A 302 1555 1555 2.31 LINK CD CD A 301 O ASP B 131 4455 1555 2.39 LINK CD CD A 302 OD2 ASP B 131 4455 1555 2.28 LINK SG CYS B 65 CD CD B1002 1555 1555 3.00 LINK NE2 HIS B 67 CD CD B1002 1555 1555 2.26 LINK OE2 GLU B 92 CD CD B1001 1555 1555 1.99 LINK OE1 GLU B 92 CD CD B1002 1555 1555 2.13 LINK OD2 ASP B 116 CD CD B1001 1555 1555 2.03 CISPEP 1 45F C 5 PRO C 6 0 3.19 SITE 1 AC1 5 CYS A 65 HIS A 67 GLU A 92 CD A 302 SITE 2 AC1 5 ASP B 131 SITE 1 AC2 5 CYS A 65 GLU A 92 ASP A 116 CD A 301 SITE 2 AC2 5 ASP B 131 SITE 1 AC3 8 GLU A 69 LYS A 71 ARG A 166 GLU A 170 SITE 2 AC3 8 HIS A 171 LEU A 172 ARG A 187 ILE A 191 SITE 1 AC4 4 CYS B 65 GLU B 92 ASP B 116 CD B1002 SITE 1 AC5 4 CYS B 65 HIS B 67 GLU B 92 CD B1001 SITE 1 AC6 3 LYS B 71 HIS B 171 LEU B 172 CRYST1 60.480 61.500 81.440 90.00 90.00 90.00 P 21 21 21 8 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 0.016534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012279 0.00000