HEADER HYDROLASE/HYDROLASE INHIBITOR 05-SEP-11 3TOG TITLE HIV-1 PROTEASE - EPOXYDIC INHIBITOR COMPLEX (PH 9 - MONOCLINIC CRYSTAL TITLE 2 FORM P21) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 501-599; COMPND 5 SYNONYM: PR160GAG-POL, MATRIX PROTEIN P17, MA, CAPSID PROTEIN P24, COMPND 6 CA, SPACER PEPTIDE P2, NUCLEOCAPSID PROTEIN P7, NC, TRANSFRAME COMPND 7 PEPTIDE, TF, P6-POL, P6*, PROTEASE, PR, RETROPEPSIN, REVERSE COMPND 8 TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEASE H, P66 RT, P51 RT, P15, COMPND 9 INTEGRASE, IN; COMPND 10 EC: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (BRU SOURCE 3 ISOLATE); SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11686; SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS HIV PR, EPOXIDE, IN-CRYSTAL REACTION, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.GEREMIA,F.M.OLAJUYIGBE,N.DEMITRI REVDAT 5 13-SEP-23 3TOG 1 REMARK SEQADV REVDAT 4 20-MAR-19 3TOG 1 JRNL REVDAT 3 08-NOV-17 3TOG 1 REMARK REVDAT 2 29-OCT-14 3TOG 1 AUTHOR REVDAT 1 15-AUG-12 3TOG 0 JRNL AUTH F.M.OLAJUYIGBE,N.DEMITRI,R.DE ZORZI,S.GEREMIA JRNL TITL DEVELOPING HIV-1 PROTEASE INHIBITORS THROUGH STEREOSPECIFIC JRNL TITL 2 REACTIONS IN PROTEIN CRYSTALS. JRNL REF MOLECULES V. 21 2016 JRNL REFN ESSN 1420-3049 JRNL PMID 27809253 JRNL DOI 10.3390/MOLECULES21111458 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 98016 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.500 REMARK 3 FREE R VALUE TEST SET COUNT : 2493 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) : 1.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6967 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE SET COUNT : 190 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3024 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.03000 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): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.063 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.053 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.195 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3194 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4327 ; 2.263 ; 2.011 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.762 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;36.945 ;24.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 578 ;14.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.914 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 521 ; 0.153 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2275 ; 0.014 ; 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): 1967 ; 1.409 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3204 ; 2.254 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1227 ; 3.432 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 5.302 ; 4.500 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3TOG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 8.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: ISOMORPHOUS STRUCTURE REMARK 200 STARTING MODEL: PDB ENTRY 2AVV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE 40%, DMSO 10%, SODIUM REMARK 280 CITRATE 0.25M. PH HAS BEEN INCREASED THROUGH AMMONIA DIFFUSION, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 9 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.06800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 EPOXYDIC INHIBITOR 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 O HOH C 126 O HOH C 156 1.52 REMARK 500 O HOH C 126 O HOH C 154 1.69 REMARK 500 O HOH A 236 O HOH A 268 1.71 REMARK 500 NH1 ARG D 8 O HOH D 241 1.88 REMARK 500 OE1 GLU A 34 O HOH A 224 1.92 REMARK 500 O HOH B 204 O HOH B 254 1.97 REMARK 500 O HOH A 258 O HOH A 259 1.99 REMARK 500 O HOH B 216 O HOH B 239 2.01 REMARK 500 O HOH B 213 O HOH B 229 2.03 REMARK 500 O HOH D 242 O HOH D 246 2.04 REMARK 500 O ILE B 50 O HOH B 202 2.13 REMARK 500 N PRO A 1 O HOH A 218 2.14 REMARK 500 OE1 GLU B 35 O HOH B 221 2.16 REMARK 500 OE1 GLU A 35 O HOH A 263 2.17 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 OE1 GLU B 21 O HOH C 147 1656 2.05 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 THR A 4 C THR A 4 O -0.120 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 ARG B 87 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP C 25 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP C 29 CB - CG - OD1 ANGL. DEV. = 5.7 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 D 34 151.49 -49.82 REMARK 500 PRO D 79 49.91 -80.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: (S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6- REMARK 630 DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO)BUTANAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 079 A 101 REMARK 630 079 D 101 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: 06Y VAL 078 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 079 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS D 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 079 D 101 DBREF 3TOG A 1 99 UNP P03367 POL_HV1BR 501 599 DBREF 3TOG B 1 99 UNP P03367 POL_HV1BR 501 599 DBREF 3TOG C 1 99 UNP P03367 POL_HV1BR 501 599 DBREF 3TOG D 1 99 UNP P03367 POL_HV1BR 501 599 SEQADV 3TOG LYS A 7 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3TOG ILE A 33 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3TOG ILE A 63 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3TOG ALA A 67 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3TOG ALA A 95 UNP P03367 CYS 595 ENGINEERED MUTATION SEQADV 3TOG LYS B 7 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3TOG ILE B 33 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3TOG ILE B 63 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3TOG ALA B 67 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3TOG ALA B 95 UNP P03367 CYS 595 ENGINEERED MUTATION SEQADV 3TOG LYS C 7 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3TOG ILE C 33 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3TOG ILE C 63 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3TOG ALA C 67 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3TOG ALA C 95 UNP P03367 CYS 595 ENGINEERED MUTATION SEQADV 3TOG LYS D 7 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3TOG ILE D 33 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3TOG ILE D 63 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3TOG ALA D 67 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3TOG ALA D 95 UNP P03367 CYS 595 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 A 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 B 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 C 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 C 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 C 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 C 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 C 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 C 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 C 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 C 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 D 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 D 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 D 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 D 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 D 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 D 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 D 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 D 99 GLN ILE GLY ALA THR LEU ASN PHE HET DMS A 100 4 HET 079 A 101 39 HET DMS B 100 4 HET DMS D 100 4 HET 079 D 101 39 HETNAM DMS DIMETHYL SULFOXIDE HETNAM 079 (S)-N-((2S,3S,4R,5R)-4-AMINO-3,5-DIHYDROXY-1,6- HETNAM 2 079 DIPHENYLHEXAN-2-YL)-3-METHYL-2-(2-PHENOXYACETAMIDO) HETNAM 3 079 BUTANAMIDE FORMUL 5 DMS 3(C2 H6 O S) FORMUL 6 079 2(C31 H39 N3 O5) FORMUL 10 HOH *269(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 GLY B 94 1 9 HELIX 3 3 GLY C 86 THR C 91 1 6 HELIX 4 4 GLY D 86 THR D 91 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 A 4 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 B 8 TRP A 42 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O GLY A 73 N ILE A 62 SHEET 4 B 8 VAL A 32 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 C 8 LYS B 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O GLN B 58 N LYS B 43 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 SHEET 4 C 8 VAL B 32 ILE B 33 1 N ILE B 33 O LEU B 76 SHEET 5 C 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 C 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 C 8 LEU B 10 ILE B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SHEET 1 D 4 GLN C 2 ILE C 3 0 SHEET 2 D 4 THR D 96 ASN D 98 -1 O LEU D 97 N ILE C 3 SHEET 3 D 4 THR C 96 ASN C 98 -1 N ASN C 98 O THR D 96 SHEET 4 D 4 GLN D 2 ILE D 3 -1 O ILE D 3 N LEU C 97 SHEET 1 E 8 LYS C 43 GLY C 49 0 SHEET 2 E 8 GLY C 52 ILE C 66 -1 O GLY C 52 N GLY C 49 SHEET 3 E 8 HIS C 69 VAL C 77 -1 O VAL C 75 N TYR C 59 SHEET 4 E 8 VAL C 32 ILE C 33 1 N ILE C 33 O LEU C 76 SHEET 5 E 8 ILE C 84 ILE C 85 -1 O ILE C 84 N VAL C 32 SHEET 6 E 8 GLN C 18 LEU C 24 1 N LEU C 23 O ILE C 85 SHEET 7 E 8 LEU C 10 ILE C 15 -1 N ILE C 13 O LYS C 20 SHEET 8 E 8 GLY C 52 ILE C 66 -1 O GLU C 65 N LYS C 14 SHEET 1 F 8 TRP D 42 GLY D 49 0 SHEET 2 F 8 GLY D 52 ILE D 66 -1 O VAL D 56 N LYS D 45 SHEET 3 F 8 HIS D 69 VAL D 77 -1 O GLY D 73 N ILE D 62 SHEET 4 F 8 VAL D 32 ILE D 33 1 N ILE D 33 O LEU D 76 SHEET 5 F 8 ILE D 84 ILE D 85 -1 O ILE D 84 N VAL D 32 SHEET 6 F 8 GLN D 18 LEU D 24 1 N LEU D 23 O ILE D 85 SHEET 7 F 8 LEU D 10 ILE D 15 -1 N ILE D 13 O LYS D 20 SHEET 8 F 8 GLY D 52 ILE D 66 -1 O GLU D 65 N LYS D 14 SITE 1 AC1 7 LYS A 14 ILE A 15 GLY A 16 GLY A 17 SITE 2 AC1 7 ILE A 63 GLU A 65 GLY B 17 SITE 1 AC2 16 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC2 16 GLY A 48 GLY A 49 ILE A 50 VAL A 82 SITE 3 AC2 16 HOH A 264 ARG B 8 LEU B 23 ASP B 25 SITE 4 AC2 16 GLY B 27 PRO B 81 VAL B 82 ILE B 84 SITE 1 AC3 8 LYS A 14 GLY A 17 LYS B 14 ILE B 15 SITE 2 AC3 8 GLY B 16 GLY B 17 ILE B 63 GLU B 65 SITE 1 AC4 8 GLY C 17 LYS D 14 ILE D 15 GLY D 16 SITE 2 AC4 8 GLY D 17 ILE D 63 ILE D 64 GLU D 65 SITE 1 AC5 18 ARG C 8 LEU C 23 ASP C 25 GLY C 27 SITE 2 AC5 18 ALA C 28 GLY C 49 ILE C 50 VAL C 82 SITE 3 AC5 18 ILE C 84 ASP D 25 GLY D 27 ALA D 28 SITE 4 AC5 18 ASP D 29 GLY D 48 GLY D 49 PRO D 81 SITE 5 AC5 18 VAL D 82 ILE D 84 CRYST1 51.191 62.136 58.751 90.00 98.73 90.00 P 1 21 1 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 0.019535 0.000000 0.003001 0.00000 SCALE2 0.000000 0.016094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017221 0.00000