HEADER VIRAL PROTEIN/PEPTIDE 09-DEC-13 3WNG TITLE CYCLIC HEXAPEPTIDE PKIDNP IN COMPLEX WITH HIV-1 INTEGRASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC CORE DOMAIN, UNP RESIDUE 1203-1359; COMPND 5 SYNONYM: HIV-1 INTEGRASE; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PKIDN(DPR) PEPTIDE; COMPND 10 CHAIN: C, D; COMPND 11 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: NL43; SOURCE 6 GENE: HIV-1 POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS DNA INTEGRATION, AIDS, INTEGRASE, ENDONUCLEASE, DNA BINDING, VIRAL KEYWDS 2 PROTEIN, LEDGF, LENS EPITHELIUM-DERIVED GROWTH FACTOR, RNASEH, POLY KEYWDS 3 NUCLEOTIDYL TRANSFERASE, VIRAL PROTEIN-PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.WIELENS,D.K.CHALMERS,M.W.PARKER REVDAT 4 30-OCT-24 3WNG 1 REMARK REVDAT 3 08-NOV-23 3WNG 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 3WNG 1 REMARK REVDAT 1 25-DEC-13 3WNG 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. 1.75 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 27545 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) : 0.176 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1450 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) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2072 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2195 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : 0.77000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.38000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.337 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2312 ; 0.021 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 96 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3142 ; 2.232 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 230 ; 0.993 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 6.800 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 93 ;35.722 ;24.839 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 376 ;14.586 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.018 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 363 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1707 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 12 ; 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 3WNG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000096555. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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) : 0.954 REMARK 200 MONOCHROMATOR : DOUBLE MIRROR REMARK 200 OPTICS : MIRRORS 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 : 27864 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 153966. REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : 0.40100 REMARK 200 FOR SHELL : 4.400 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: 3L3U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 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 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 68.47333 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 34.23667 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: 6300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -167.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE PKIDN(DPR) PEPTIDE IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: PKIDN(DPR) PEPTIDE REMARK 400 CHAIN: C, D 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 SER A 56 REMARK 465 GLU A 138 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 GLY A 190 REMARK 465 ILE A 191 REMARK 465 THR A 210 REMARK 465 LYS A 211 REMARK 465 GLU A 212 REMARK 465 GLU B 138 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 ILE B 151 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 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 ARG A 127 NE CZ NH1 NH2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS B 188 CG CD CE NZ 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 ND2 ASN A 117 O HOH A 1169 1.98 REMARK 500 CE1 HIS A 183 O HOH A 1165 2.14 REMARK 500 O HOH B 450 O HOH B 461 2.17 REMARK 500 CE1 HIS B 183 O HOH B 470 2.18 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 114 CG HIS A 114 CD2 0.055 REMARK 500 TRP B 132 CE2 TRP B 132 CD2 0.074 REMARK 500 ASN C 5 C DPR C 6 N 0.147 REMARK 500 ASN D 5 C DPR D 6 N 0.133 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 GLU B 92 OE1 - CD - OE2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER B 57 7.29 -69.40 REMARK 500 ASN C 5 139.02 177.28 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 118.9 REMARK 620 3 GLU A 92 OE1 98.2 95.3 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 90.0 REMARK 620 3 ASP A 116 OD2 103.9 160.2 REMARK 620 4 HOH A1101 O 167.7 82.3 81.6 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 CYS B 65 SG REMARK 620 2 HIS B 67 NE2 119.8 REMARK 620 3 GLU B 92 OE1 101.2 92.6 REMARK 620 N 1 2 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 CYS B 65 SG REMARK 620 2 GLU B 92 OE2 89.9 REMARK 620 3 ASP B 116 OD2 103.0 161.0 REMARK 620 4 HOH B 401 O 167.1 82.9 81.8 REMARK 620 N 1 2 3 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 SO4 A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF PKIDN(DPR) PEPTIDE REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF PKIDN(DPR) PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WNE RELATED DB: PDB REMARK 900 RELATED ID: 3WNF RELATED DB: PDB REMARK 900 RELATED ID: 3WNH RELATED DB: PDB DBREF 3WNG A 56 212 UNP P12497 POL_HV1N5 1203 1359 DBREF 3WNG B 56 212 UNP P12497 POL_HV1N5 1203 1359 DBREF 3WNG C 1 6 PDB 3WNG 3WNG 1 6 DBREF 3WNG D 1 6 PDB 3WNG 3WNG 1 6 SEQADV 3WNG SER A 56 UNP P12497 CYS 1203 ENGINEERED MUTATION SEQADV 3WNG GLY A 123 UNP P12497 SER 1270 ENGINEERED MUTATION SEQADV 3WNG ALA A 124 UNP P12497 THR 1271 ENGINEERED MUTATION SEQADV 3WNG ARG A 127 UNP P12497 LYS 1274 ENGINEERED MUTATION SEQADV 3WNG ASP A 131 UNP P12497 TRP 1278 ENGINEERED MUTATION SEQADV 3WNG ASP A 139 UNP P12497 PHE 1286 ENGINEERED MUTATION SEQADV 3WNG HIS A 185 UNP P12497 PHE 1332 ENGINEERED MUTATION SEQADV 3WNG SER B 56 UNP P12497 CYS 1203 ENGINEERED MUTATION SEQADV 3WNG GLY B 123 UNP P12497 SER 1270 ENGINEERED MUTATION SEQADV 3WNG ALA B 124 UNP P12497 THR 1271 ENGINEERED MUTATION SEQADV 3WNG ARG B 127 UNP P12497 LYS 1274 ENGINEERED MUTATION SEQADV 3WNG ASP B 131 UNP P12497 TRP 1278 ENGINEERED MUTATION SEQADV 3WNG ASP B 139 UNP P12497 PHE 1286 ENGINEERED MUTATION SEQADV 3WNG HIS B 185 UNP P12497 PHE 1332 ENGINEERED MUTATION SEQRES 1 A 157 SER SER PRO GLY ILE TRP GLN LEU ASP CYS THR HIS LEU SEQRES 2 A 157 GLU GLY LYS VAL ILE LEU VAL ALA VAL HIS VAL ALA SER SEQRES 3 A 157 GLY TYR ILE GLU ALA GLU VAL ILE PRO ALA GLU THR GLY SEQRES 4 A 157 GLN GLU THR ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG SEQRES 5 A 157 TRP PRO VAL LYS THR VAL HIS THR ASP ASN GLY SER ASN SEQRES 6 A 157 PHE THR GLY ALA THR VAL ARG ALA ALA CYS ASP TRP ALA SEQRES 7 A 157 GLY ILE LYS GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SEQRES 8 A 157 SER GLN GLY VAL ILE GLU SER MET ASN LYS GLU LEU LYS SEQRES 9 A 157 LYS ILE ILE GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU SEQRES 10 A 157 LYS THR ALA VAL GLN MET ALA VAL PHE ILE HIS ASN HIS SEQRES 11 A 157 LYS ARG LYS GLY GLY ILE GLY GLY TYR SER ALA GLY GLU SEQRES 12 A 157 ARG ILE VAL ASP ILE ILE ALA THR ASP ILE GLN THR LYS SEQRES 13 A 157 GLU SEQRES 1 B 157 SER SER PRO GLY ILE TRP GLN LEU ASP CYS THR HIS LEU SEQRES 2 B 157 GLU GLY LYS VAL ILE LEU VAL ALA VAL HIS VAL ALA SER SEQRES 3 B 157 GLY TYR ILE GLU ALA GLU VAL ILE PRO ALA GLU THR GLY SEQRES 4 B 157 GLN GLU THR ALA TYR PHE LEU LEU LYS LEU ALA GLY ARG SEQRES 5 B 157 TRP PRO VAL LYS THR VAL HIS THR ASP ASN GLY SER ASN SEQRES 6 B 157 PHE THR GLY ALA THR VAL ARG ALA ALA CYS ASP TRP ALA SEQRES 7 B 157 GLY ILE LYS GLN GLU ASP GLY ILE PRO TYR ASN PRO GLN SEQRES 8 B 157 SER GLN GLY VAL ILE GLU SER MET ASN LYS GLU LEU LYS SEQRES 9 B 157 LYS ILE ILE GLY GLN VAL ARG ASP GLN ALA GLU HIS LEU SEQRES 10 B 157 LYS THR ALA VAL GLN MET ALA VAL PHE ILE HIS ASN HIS SEQRES 11 B 157 LYS ARG LYS GLY GLY ILE GLY GLY TYR SER ALA GLY GLU SEQRES 12 B 157 ARG ILE VAL ASP ILE ILE ALA THR ASP ILE GLN THR LYS SEQRES 13 B 157 GLU SEQRES 1 C 6 PRO LYS ILE ASP ASN DPR SEQRES 1 D 6 PRO LYS ILE ASP ASN DPR HET DPR C 6 7 HET DPR D 6 7 HET CD A1001 1 HET CD A1002 1 HET CL A1003 1 HET SO4 A1004 5 HET SO4 A1005 5 HET SO4 A1006 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 HET SO4 B 306 5 HETNAM DPR D-PROLINE HETNAM CD CADMIUM ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION FORMUL 3 DPR 2(C5 H9 N O2) FORMUL 5 CD 4(CD 2+) FORMUL 7 CL 2(CL 1-) FORMUL 8 SO4 6(O4 S 2-) FORMUL 17 HOH *154(H2 O) HELIX 1 1 THR A 93 TRP A 108 1 16 HELIX 2 2 GLY A 118 THR A 122 5 5 HELIX 3 3 ALA A 124 GLY A 134 1 11 HELIX 4 4 GLU A 152 ARG A 166 1 15 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 GLY B 118 THR B 122 5 5 HELIX 10 10 ALA B 124 GLY B 134 1 11 HELIX 11 11 SER B 153 ARG B 166 1 14 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 ILE B 208 1 14 SHEET 1 A 4 ILE A 84 ILE A 89 0 SHEET 2 A 4 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 A 4 ILE A 60 LEU A 68 -1 N GLN A 62 O VAL A 77 SHEET 4 A 4 THR A 112 HIS A 114 1 O HIS A 114 N LEU A 63 SHEET 1 B 4 ILE B 84 ILE B 89 0 SHEET 2 B 4 LYS B 71 HIS B 78 -1 N ALA B 76 O GLU B 85 SHEET 3 B 4 ILE B 60 LEU B 68 -1 N GLN B 62 O VAL B 77 SHEET 4 B 4 THR B 112 HIS B 114 1 O THR B 112 N TRP B 61 LINK N PRO C 1 C DPR C 6 1555 1555 1.51 LINK C ASN C 5 N DPR C 6 1555 1555 1.49 LINK N PRO D 1 C DPR D 6 1555 1555 1.51 LINK C ASN D 5 N DPR D 6 1555 1555 1.47 LINK SG CYS A 65 CD CD A1001 1555 1555 2.52 LINK SG CYS A 65 CD CD A1002 1555 1555 2.53 LINK NE2 HIS A 67 CD CD A1001 1555 1555 2.13 LINK OE1 GLU A 92 CD CD A1001 1555 1555 2.05 LINK OE2 GLU A 92 CD CD A1002 1555 1555 2.46 LINK OD2 ASP A 116 CD CD A1002 1555 1555 2.45 LINK CD CD A1002 O HOH A1101 1555 1555 2.42 LINK SG CYS B 65 CD CD B 301 1555 1555 2.53 LINK SG CYS B 65 CD CD B 302 1555 1555 2.57 LINK NE2 HIS B 67 CD CD B 301 1555 1555 2.17 LINK OE1 GLU B 92 CD CD B 301 1555 1555 1.90 LINK OE2 GLU B 92 CD CD B 302 1555 1555 2.45 LINK OD2 ASP B 116 CD CD B 302 1555 1555 2.42 LINK CD CD B 302 O HOH B 401 1555 1555 2.36 SITE 1 AC1 4 CYS A 65 HIS A 67 GLU A 92 ASP B 131 SITE 1 AC2 6 CYS A 65 GLU A 92 ASP A 116 CL A1003 SITE 2 AC2 6 HOH A1101 HOH B 408 SITE 1 AC3 4 CYS A 65 ASP A 116 ASN A 120 CD A1002 SITE 1 AC4 7 LYS A 71 ARG A 166 GLU A 170 HIS A 171 SITE 2 AC4 7 LEU A 172 HOH A1117 HOH A1127 SITE 1 AC5 5 THR A 66 HIS A 67 GLU A 152 LYS A 159 SITE 2 AC5 5 ARG B 127 SITE 1 AC6 7 GLY A 123 ALA A 124 THR A 125 HOH A1107 SITE 2 AC6 7 HOH A1108 HOH A1119 HOH A1125 SITE 1 AC7 4 ASP A 131 CYS B 65 HIS B 67 GLU B 92 SITE 1 AC8 6 HOH A1105 CYS B 65 GLU B 92 ASP B 116 SITE 2 AC8 6 CL B 303 HOH B 401 SITE 1 AC9 4 CYS B 65 ASP B 116 ASN B 120 CD B 302 SITE 1 BC1 7 LYS B 71 ARG B 166 GLU B 170 HIS B 171 SITE 2 BC1 7 LEU B 172 HOH B 418 HOH B 435 SITE 1 BC2 6 GLY B 123 ALA B 124 THR B 125 HOH B 407 SITE 2 BC2 6 HOH B 419 HOH B 428 SITE 1 BC3 4 THR B 66 HIS B 67 GLU B 152 LYS B 159 SITE 1 BC4 8 GLN A 95 THR A 125 ASP B 167 GLN B 168 SITE 2 BC4 8 ALA B 169 GLU B 170 HIS B 171 THR B 174 SITE 1 BC5 9 ASP A 167 GLN A 168 ALA A 169 GLU A 170 SITE 2 BC5 9 HIS A 171 THR A 174 GLN B 95 THR B 125 SITE 3 BC5 9 HOH D 101 CRYST1 50.250 50.250 102.710 90.00 90.00 120.00 P 32 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 0.019900 0.011490 0.000000 0.00000 SCALE2 0.000000 0.022979 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009736 0.00000