HEADER HYDROLASE/HYDROLASE INHIBITOR 08-JUN-10 3NDU TITLE HIV-1 PROTEASE SAQUINAVIR:RITONAVIR 1:5 COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.4.23.16; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV-1 PROTEASE, HYDROLASE, AIDS, ASPARTYL PROTEASE, SAQUINAVIR, KEYWDS 2 CARBAMYLATION, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.GEREMIA,F.M.OLAJUYIGBE,N.DEMITRI REVDAT 3 06-SEP-23 3NDU 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 HETSYN LINK REVDAT 2 07-DEC-11 3NDU 1 JRNL REVDAT 1 20-JUL-11 3NDU 0 JRNL AUTH F.M.OLAJUYIGBE,N.DEMITRI,S.GEREMIA JRNL TITL INVESTIGATION OF 2-FOLD DISORDER OF INHIBITORS AND RELATIVE JRNL TITL 2 POTENCY BY CRYSTALLIZATIONS OF HIV-1 PROTEASE IN RITONAVIR JRNL TITL 3 AND SAQUINAVIR MIXTURES JRNL REF CRYST.GROWTH DES. V. 11 4378 2011 JRNL REFN ISSN 1528-7483 JRNL DOI 10.1021/CG200514Z REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.142 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.136 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5004 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 95332 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.130 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 70768 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 161 REMARK 3 SOLVENT ATOMS : 262 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3452.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 62 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 34311 REMARK 3 NUMBER OF RESTRAINTS : 46294 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.122 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.091 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000059704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 REMARK 200 OPTICS : NULL 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 : 70768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: SHELX REMARK 200 STARTING MODEL: 3K4V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, DMSO, SODIUM REMARK 280 CITRATE, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 31.35250 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: 7420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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: 6100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 ARF C 0 REMARK 465 ARF D 0 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 A 58 NE - CZ - NH1 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 PHE A 100 N - CA - CB ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG B 9 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 ARG B 9 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 MET B 47 CG - SD - CE ANGL. DEV. = 10.7 DEGREES REMARK 500 ILE C 50 CA - C - N ANGL. DEV. = 15.8 DEGREES REMARK 500 ARG C 57 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 PHE C 99 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG D 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG D 41 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 MET D 46 CG - SD - CE ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG D 57 CG - CD - NE ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG D 57 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG D 87 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES 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 NA B1020 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 94 O REMARK 620 2 PHE B 100 OXT 128.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1015 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 112 O REMARK 620 2 ACT A1007 O 124.0 REMARK 620 N 1 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- REMARK 630 BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3- REMARK 630 HYDROXY-1 -PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO) REMARK 630 BUTANEDIAMIDE 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 ROC A 101 REMARK 630 ROC D 100 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: QNC ASN HP0 NTB 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 ROC A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1012 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1015 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1017 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1021 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1014 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1016 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1020 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS C 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 1013 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROC D 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS D 101 DBREF 3NDU A 2 100 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 DBREF 3NDU B 2 100 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 DBREF 3NDU C 1 99 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 DBREF 3NDU D 1 99 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 SEQADV 3NDU ARF A 1 UNP Q7SSI0 INSERTION SEQADV 3NDU LYS A 8 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 3NDU ILE A 34 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 3NDU ILE A 64 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 3NDU ALA A 68 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 3NDU ALA A 96 UNP Q7SSI0 SER 95 ENGINEERED MUTATION SEQADV 3NDU ARF B 1 UNP Q7SSI0 INSERTION SEQADV 3NDU LYS B 8 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 3NDU ILE B 34 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 3NDU ILE B 64 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 3NDU ALA B 68 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 3NDU ALA B 96 UNP Q7SSI0 SER 95 ENGINEERED MUTATION SEQADV 3NDU ARF C 0 UNP Q7SSI0 INSERTION SEQADV 3NDU LYS C 7 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 3NDU ILE C 33 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 3NDU ILE C 63 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 3NDU ALA C 67 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 3NDU ALA C 95 UNP Q7SSI0 SER 95 ENGINEERED MUTATION SEQADV 3NDU ARF D 0 UNP Q7SSI0 INSERTION SEQADV 3NDU LYS D 7 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 3NDU ILE D 33 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 3NDU ILE D 63 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 3NDU ALA D 67 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 3NDU ALA D 95 UNP Q7SSI0 SER 95 ENGINEERED MUTATION SEQRES 1 A 100 ARF PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR SEQRES 2 A 100 ILE LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP SEQRES 3 A 100 THR GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU SEQRES 4 A 100 PRO GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY SEQRES 5 A 100 GLY PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE SEQRES 6 A 100 GLU ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL SEQRES 7 A 100 GLY PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU SEQRES 8 A 100 THR GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 B 100 ARF PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR SEQRES 2 B 100 ILE LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP SEQRES 3 B 100 THR GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU SEQRES 4 B 100 PRO GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY SEQRES 5 B 100 GLY PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE SEQRES 6 B 100 GLU ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL SEQRES 7 B 100 GLY PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU SEQRES 8 B 100 THR GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 C 100 ARF PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR SEQRES 2 C 100 ILE LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP SEQRES 3 C 100 THR GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU SEQRES 4 C 100 PRO GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY SEQRES 5 C 100 GLY PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE SEQRES 6 C 100 GLU ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL SEQRES 7 C 100 GLY PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU SEQRES 8 C 100 THR GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 D 100 ARF PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR SEQRES 2 D 100 ILE LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP SEQRES 3 D 100 THR GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU SEQRES 4 D 100 PRO GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY SEQRES 5 D 100 GLY PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE SEQRES 6 D 100 GLU ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL SEQRES 7 D 100 GLY PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU SEQRES 8 D 100 THR GLN ILE GLY ALA THR LEU ASN PHE HET ARF A 1 3 HET ARF B 1 3 HET ROC A 101 98 HET DMS A 102 4 HET ACT A1007 4 HET CL A1010 1 HET GOL A1012 6 HET NA A1015 2 HET ACT A1017 4 HET CL A1021 2 HET DMS B 101 4 HET GOL B1001 6 HET CL B1003 1 HET CL B1005 1 HET NA B1014 1 HET ACT B1016 4 HET NA B1020 1 HET DMS C 100 4 HET DMS C 101 4 HET CL C1004 1 HET CL C1006 1 HET ACT C1008 4 HET GOL C1013 6 HET ROC D 100 98 HET DMS D 101 8 HETNAM ARF FORMAMIDE HETNAM ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- HETNAM 2 ROC BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H- HETNAM 3 ROC ISOQUINOLIN-2-YL]-3-HYDROXY-1 -PHENYL-BUTAN-2-YL]-2- HETNAM 4 ROC (QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN ROC FORTOVASE; SAQUINAVIR; RO 31-8959 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 ARF 2(C H3 N O) FORMUL 5 ROC 2(C38 H50 N6 O5) FORMUL 6 DMS 5(C2 H6 O S) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 8 CL 6(CL 1-) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 10 NA 3(NA 1+) FORMUL 28 HOH *262(H2 O) HELIX 1 1 GLY A 87 THR A 92 1 6 HELIX 2 2 GLY B 87 GLY B 95 1 9 HELIX 3 3 GLY C 86 THR C 91 1 6 HELIX 4 4 GLY D 86 GLY D 94 1 9 SHEET 1 A 4 GLN A 3 ILE A 4 0 SHEET 2 A 4 THR B 97 ASN B 99 -1 O LEU B 98 N ILE A 4 SHEET 3 A 4 THR A 97 ASN A 99 -1 N THR A 97 O ASN B 99 SHEET 4 A 4 GLN B 3 ILE B 4 -1 O ILE B 4 N LEU A 98 SHEET 1 B 8 LYS A 44 GLY A 50 0 SHEET 2 B 8 GLY A 53 ILE A 67 -1 O GLN A 59 N LYS A 44 SHEET 3 B 8 HIS A 70 GLY A 79 -1 O VAL A 78 N ARG A 58 SHEET 4 B 8 VAL A 33 GLU A 35 1 N ILE A 34 O LEU A 77 SHEET 5 B 8 ILE A 85 ILE A 86 -1 O ILE A 85 N VAL A 33 SHEET 6 B 8 GLN A 19 LEU A 25 1 N LEU A 24 O ILE A 86 SHEET 7 B 8 LEU A 11 ILE A 16 -1 N ILE A 14 O LYS A 21 SHEET 8 B 8 GLY A 53 ILE A 67 -1 O GLU A 66 N LYS A 15 SHEET 1 C 8 LYS B 44 GLY B 50 0 SHEET 2 C 8 GLY B 53 ILE B 67 -1 O GLN B 59 N LYS B 44 SHEET 3 C 8 HIS B 70 VAL B 78 -1 O HIS B 70 N ILE B 67 SHEET 4 C 8 VAL B 33 ILE B 34 1 N ILE B 34 O LEU B 77 SHEET 5 C 8 ILE B 85 ILE B 86 -1 O ILE B 85 N VAL B 33 SHEET 6 C 8 GLN B 19 LEU B 25 1 N LEU B 24 O ILE B 86 SHEET 7 C 8 LEU B 11 ILE B 16 -1 N ILE B 14 O LYS B 21 SHEET 8 C 8 GLY B 53 ILE B 67 -1 O GLU B 66 N LYS B 15 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 TRP C 42 GLY C 49 0 SHEET 2 E 8 GLY C 52 ILE C 66 -1 O GLN C 58 N LYS C 43 SHEET 3 E 8 HIS C 69 VAL C 77 -1 O HIS C 69 N ILE C 66 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 LYS D 43 GLY D 49 0 SHEET 2 F 8 GLY D 52 ILE D 66 -1 O GLN D 58 N LYS D 43 SHEET 3 F 8 HIS D 69 VAL D 77 -1 O HIS D 69 N ILE D 66 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 LINK C ARF A 1 N PRO A 2 1555 1555 1.34 LINK C ARF B 1 N PRO B 2 1555 1555 1.33 LINK O ILE A 94 NA NA B1020 1555 1555 2.73 LINK O HOH A 112 NA A NA A1015 1555 1555 2.75 LINK O ACT A1007 NA A NA A1015 1555 1555 3.05 LINK OD2 ASP B 61 NA NA B1014 1555 1555 2.34 LINK OXT PHE B 100 NA NA B1020 1555 1555 2.05 SITE 1 AC1 32 ARG A 9 ASP A 26 GLY A 28 ALA A 29 SITE 2 AC1 32 ASP A 30 ASP A 31 ILE A 48 GLY A 49 SITE 3 AC1 32 GLY A 50 ILE A 51 THR A 81 PRO A 82 SITE 4 AC1 32 ILE A 85 HOH A 119 HOH A 570 ARG B 9 SITE 5 AC1 32 ASP B 26 GLY B 28 ALA B 29 ASP B 30 SITE 6 AC1 32 ASP B 31 GLY B 49 GLY B 50 ILE B 51 SITE 7 AC1 32 THR B 81 PRO B 82 VAL B 83 ILE B 85 SITE 8 AC1 32 HOH B 103 HOH B 107 HOH B 153 TRP C 6 SITE 1 AC2 6 LYS A 15 ILE A 16 GLY A 18 ILE A 64 SITE 2 AC2 6 GLY B 18 DMS B 101 SITE 1 AC3 5 THR A 13 GLU A 66 ALA A 68 GLY A 69 SITE 2 AC3 5 NA A1015 SITE 1 AC4 1 LYS B 71 SITE 1 AC5 3 GLN A 3 ILE A 4 THR A 5 SITE 1 AC6 3 GLY A 69 HOH A 112 ACT A1007 SITE 1 AC7 2 TRP A 7 ARG B 88 SITE 1 AC8 3 LYS A 44 LYS A 46 GLN A 59 SITE 1 AC9 8 LYS A 15 GLY A 18 DMS A 102 LYS B 15 SITE 2 AC9 8 ILE B 16 GLY B 17 GLY B 18 ILE B 64 SITE 1 BC1 5 LYS B 46 MET B 47 HOH B 104 HOH B 212 SITE 2 BC1 5 HOH D 107 SITE 1 BC2 1 SER B 38 SITE 1 BC3 1 SER A 38 SITE 1 BC4 1 ASP B 61 SITE 1 BC5 5 LEU B 11 VAL B 12 THR B 13 HOH B 576 SITE 2 BC5 5 TRP C 42 SITE 1 BC6 3 HIS A 70 ILE A 94 PHE B 100 SITE 1 BC7 6 LYS C 14 GLY C 16 GLY C 17 ILE C 63 SITE 2 BC7 6 GLY D 17 DMS D 101 SITE 1 BC8 5 MET C 36 SER C 37 PRO D 39 GLY D 40 SITE 2 BC8 5 HOH D 203 SITE 1 BC9 3 LYS A 71 LYS B 15 LYS C 55 SITE 1 CC1 5 THR C 4 TRP C 6 HOH C 301 THR D 91 SITE 2 CC1 5 GLY D 94 SITE 1 CC2 4 PRO C 79 HOH C 578 GLY D 51 HOH D 541 SITE 1 CC3 31 ARG C 8 ASP C 25 GLY C 27 ALA C 28 SITE 2 CC3 31 ASP C 29 ASP C 30 VAL C 32 ILE C 47 SITE 3 CC3 31 GLY C 48 GLY C 49 ILE C 50 THR C 80 SITE 4 CC3 31 PRO C 81 ILE C 84 HOH C 129 HOH C 573 SITE 5 CC3 31 ASP D 25 GLY D 27 ALA D 28 ASP D 29 SITE 6 CC3 31 ASP D 30 VAL D 32 ILE D 47 GLY D 48 SITE 7 CC3 31 GLY D 49 ILE D 50 THR D 80 PRO D 81 SITE 8 CC3 31 ILE D 84 HOH D 115 HOH D 150 SITE 1 CC4 8 GLY C 17 DMS C 100 LYS D 14 ILE D 15 SITE 2 CC4 8 GLY D 16 GLY D 17 ILE D 63 GLU D 65 CRYST1 51.190 62.705 59.296 90.00 98.32 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 0.002857 0.00000 SCALE2 0.000000 0.015948 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017044 0.00000 HETATM 1 N ARF A 1 7.593 -6.607 39.331 1.00 34.35 N ANISOU 1 N ARF A 1 5909 2780 4362 -343 2478 -172 N HETATM 2 C ARF A 1 8.265 -6.909 38.216 1.00 27.39 C ANISOU 2 C ARF A 1 3214 3518 3675 308 435 -1322 C HETATM 3 O ARF A 1 9.389 -7.454 38.200 1.00 30.39 O ANISOU 3 O ARF A 1 3070 3246 5230 111 -150 -886 O