HEADER TRANSFERASE/TRANSFERASE BINDING PROTEIN 07-FEB-15 4Y1D 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: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 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 4 15-NOV-23 4Y1D 1 LINK REVDAT 3 27-SEP-23 4Y1D 1 REMARK SEQADV LINK REVDAT 2 01-JUN-16 4Y1D 1 SOURCE REMARK REVDAT 1 13-MAY-15 4Y1D 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. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 22668 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1194 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1408 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2235 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 2.26000 REMARK 3 B33 (A**2) : -1.89000 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): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.595 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2292 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 49 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3103 ; 2.056 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 114 ; 1.303 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.989 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;35.604 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;18.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 9.360 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.155 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1673 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 7 ; 0.001 ; 0.020 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 4Y1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206686. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-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 : 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 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 94.3 REMARK 200 DATA REDUNDANCY : 6.720 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: 3WNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.15M SODIUM REMARK 280 CITRATE, 5MM CADMIUM CHLORIDE, PH 4.6, VAPOR DIFFUSION, HANGING REMARK 280 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 30.40000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.40000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.30000 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: 5120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 SER A 56 REMARK 465 ASP A 139 REMARK 465 GLY A 140 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 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 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 GLY B 189 REMARK 465 GLY B 190 REMARK 465 ILE B 191 REMARK 465 GLY B 192 REMARK 465 ILE B 208 REMARK 465 GLN B 209 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: 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 67 CG HIS A 67 CD2 0.056 REMARK 500 HIS B 67 CG HIS B 67 CD2 0.059 REMARK 500 ARG B 107 CZ ARG B 107 NH1 0.080 REMARK 500 ARG B 107 CZ ARG B 107 NH2 0.082 REMARK 500 HIS B 183 CG HIS B 183 CD2 0.070 REMARK 500 ASP D 3 C ASN D 4 N 0.141 REMARK 500 ASN D 4 C DVA D 5 N 0.149 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 PRO B 145 C - N - CD ANGL. DEV. = -14.0 DEGREES REMARK 500 ASP B 207 CB - CG - OD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP D 3 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DVA D 5 CA - C - N ANGL. DEV. = 16.3 DEGREES REMARK 500 DVA D 5 O - C - N ANGL. DEV. = -15.8 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 A 117 -0.81 66.08 REMARK 500 ASN B 144 165.63 85.69 REMARK 500 ASN D 4 -43.15 -17.30 REMARK 500 DVA D 5 -157.89 -63.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 144 PRO B 145 -130.87 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 A1001 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 HIS A 67 NE2 112.2 REMARK 620 3 GLU A 92 OE1 106.2 84.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A1002 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 GLU A 92 OE2 100.7 REMARK 620 3 ASP A 116 OD2 97.4 156.5 REMARK 620 4 HOH A1107 O 161.3 75.5 82.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 O REMARK 620 2 ASP A 131 OD1 79.8 REMARK 620 3 HOH A1147 O 37.7 92.0 REMARK 620 4 CYS B 65 SG 34.4 94.2 4.9 REMARK 620 5 HIS B 67 NE2 34.3 87.7 4.8 6.8 REMARK 620 6 GLU B 92 OE1 30.3 89.3 7.4 5.5 5.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 CYS B 65 SG 66.5 REMARK 620 3 GLU B 92 OE2 62.2 4.8 REMARK 620 4 ASP B 116 OD2 65.2 4.2 6.9 REMARK 620 5 HOH B 405 O 61.7 4.8 2.9 4.8 REMARK 620 N 1 2 3 4 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 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Ligand residues DVA D 5 through REMARK 800 ASP D 3 bound to ASN D 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y1C RELATED DB: PDB DBREF 4Y1D A 50 212 UNP F2WR39 F2WR39_9HIV1 50 212 DBREF 4Y1D B 50 212 UNP F2WR39 F2WR39_9HIV1 50 212 DBREF 4Y1D D 1 6 PDB 4Y1D 4Y1D 1 6 SEQADV 4Y1D MET A 46 UNP F2WR39 INITIATING METHIONINE SEQADV 4Y1D GLY A 47 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D SER A 48 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D HIS A 49 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D SER A 56 UNP F2WR39 CYS 56 ENGINEERED MUTATION SEQADV 4Y1D ASP A 131 UNP F2WR39 TRP 131 ENGINEERED MUTATION SEQADV 4Y1D ASP A 139 UNP F2WR39 PHE 139 ENGINEERED MUTATION SEQADV 4Y1D HIS A 185 UNP F2WR39 PHE 185 ENGINEERED MUTATION SEQADV 4Y1D MET B 46 UNP F2WR39 INITIATING METHIONINE SEQADV 4Y1D GLY B 47 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D SER B 48 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D HIS B 49 UNP F2WR39 EXPRESSION TAG SEQADV 4Y1D SER B 56 UNP F2WR39 CYS 56 ENGINEERED MUTATION SEQADV 4Y1D ASP B 131 UNP F2WR39 TRP 131 ENGINEERED MUTATION SEQADV 4Y1D ASP B 139 UNP F2WR39 PHE 139 ENGINEERED MUTATION SEQADV 4Y1D HIS B 185 UNP F2WR39 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 D 6 LYS NLE ASP ASN DVA 45W HET NLE D 2 8 HET DVA D 5 7 HET 45W D 6 10 HET CD A1001 1 HET CD A1002 1 HET CL A1003 1 HET SO4 A1004 5 HET SO4 A1005 5 HET CD B 301 1 HET CD B 302 1 HET CL B 303 1 HET SO4 B 304 5 HET SO4 B 305 5 HETNAM NLE NORLEUCINE HETNAM DVA D-VALINE HETNAM 45W (4S)-4-(ETHYNYLOXY)-D-PROLINE HETNAM CD CADMIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 NLE C6 H13 N O2 FORMUL 3 DVA C5 H11 N O2 FORMUL 3 45W C7 H9 N O3 FORMUL 4 CD 4(CD 2+) FORMUL 6 CL 2(CL 1-) FORMUL 7 SO4 4(O4 S 2-) FORMUL 14 HOH *106(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 GLY A 134 1 12 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 SER A 195 GLN A 209 1 15 HELIX 8 AA8 THR B 93 TRP B 108 1 16 HELIX 9 AA9 GLY B 118 SER B 123 1 6 HELIX 10 AB1 SER B 123 GLY B 134 1 12 HELIX 11 AB2 GLU B 152 ARG B 166 1 15 HELIX 12 AB3 ASP B 167 ALA B 169 5 3 HELIX 13 AB4 HIS B 171 LYS B 186 1 16 HELIX 14 AB5 SER B 195 ALA B 205 1 11 SHEET 1 AA1 4 ILE A 84 ILE A 89 0 SHEET 2 AA1 4 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 AA1 4 ILE A 60 LEU A 68 -1 N ASP A 64 O VAL A 75 SHEET 4 AA1 4 THR A 112 HIS A 114 1 O HIS A 114 N TRP A 61 SHEET 1 AA2 5 ILE B 84 ILE B 89 0 SHEET 2 AA2 5 LYS B 71 HIS B 78 -1 N VAL B 72 O ILE B 89 SHEET 3 AA2 5 ILE B 60 LEU B 68 -1 N LEU B 68 O LYS B 71 SHEET 4 AA2 5 THR B 112 THR B 115 1 O THR B 112 N TRP B 61 SHEET 5 AA2 5 LYS B 136 ASP B 139 1 O GLU B 138 N VAL B 113 LINK C LYS D 1 N NLE D 2 1555 1555 1.46 LINK N LYS D 1 C 45W D 6 1555 1555 1.50 LINK C NLE D 2 N ASP D 3 1555 1555 1.43 LINK C ASN D 4 N DVA D 5 1555 1555 1.49 LINK C DVA D 5 N 45W D 6 1555 1555 1.47 LINK SG CYS A 65 CD CD A1001 1555 1555 2.62 LINK SG CYS A 65 CD CD A1002 1555 1555 2.52 LINK NE2 HIS A 67 CD CD A1001 1555 1555 2.24 LINK OE1 GLU A 92 CD CD A1001 1555 1555 1.98 LINK OE2 GLU A 92 CD CD A1002 1555 1555 2.19 LINK OD2 ASP A 116 CD CD A1002 1555 1555 2.10 LINK O ASP A 131 CD CD B 301 1555 4556 2.38 LINK OD1 ASP A 131 CD CD B 301 1555 4556 2.44 LINK OD1 ASP A 131 CD CD B 302 1555 4556 2.49 LINK CD CD A1002 O HOH A1107 1555 1555 2.57 LINK O HOH A1147 CD CD B 301 4456 1555 2.50 LINK SG CYS B 65 CD CD B 301 1555 1555 2.49 LINK SG CYS B 65 CD CD B 302 1555 1555 2.56 LINK NE2 HIS B 67 CD CD B 301 1555 1555 2.31 LINK OE1 GLU B 92 CD CD B 301 1555 1555 2.12 LINK OE2 GLU B 92 CD CD B 302 1555 1555 2.17 LINK OD2 ASP B 116 CD CD B 302 1555 1555 2.42 LINK CD CD B 302 O HOH B 405 1555 1555 2.36 CISPEP 1 DVA D 5 45W D 6 0 -1.20 SITE 1 AC1 4 CYS A 65 HIS A 67 GLU A 92 CD A1002 SITE 1 AC2 6 CYS A 65 GLU A 92 ASP A 116 CD A1001 SITE 2 AC2 6 CL A1003 HOH A1107 SITE 1 AC3 3 ASP A 116 PHE A 121 CD A1002 SITE 1 AC4 5 LYS A 71 HIS A 171 LEU A 172 HOH A1135 SITE 2 AC4 5 HOH A1145 SITE 1 AC5 3 CYS A 65 THR A 66 HIS A 67 SITE 1 AC6 6 ASP A 131 HOH A1147 CYS B 65 HIS B 67 SITE 2 AC6 6 GLU B 92 CD B 302 SITE 1 AC7 7 ASP A 131 CYS B 65 GLU B 92 ASP B 116 SITE 2 AC7 7 CD B 301 CL B 303 HOH B 405 SITE 1 AC8 5 CYS B 65 GLU B 92 ASP B 116 PHE B 121 SITE 2 AC8 5 CD B 302 SITE 1 AC9 8 GLU B 69 LYS B 71 ARG B 166 GLU B 170 SITE 2 AC9 8 HIS B 171 LEU B 172 ARG B 187 HOH B 432 SITE 1 AD1 4 LYS A 136 THR B 66 HIS B 67 LYS B 159 SITE 1 AD2 9 GLN A 168 ALA A 169 GLU A 170 HIS A 171 SITE 2 AD2 9 THR A 174 HOH A1109 THR B 125 ASN D 4 SITE 3 AD2 9 HOH D 101 CRYST1 60.800 62.600 82.000 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 0.016447 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012195 0.00000