HEADER HYDROLASE/HYDROLASE INHIBITOR 08-JUN-10 3NDT TITLE HIV-1 PROTEASE SAQUINAVIR:RITONAVIR 1:1 COMPLEX STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PR, RETROPEPSIN; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 BH10; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, AIDS, ASPARTYL PROTEASE, CARBAMYLATION, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.GEREMIA,F.M.OLAJUYIGBE,N.DEMITRI REVDAT 3 06-SEP-23 3NDT 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 HETSYN LINK REVDAT 2 07-DEC-11 3NDT 1 JRNL REVDAT 1 20-JUL-11 3NDT 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. 1.72 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 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) : 0.128 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.140 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1750 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 34735 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.110 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)) : 24746 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 : 123 REMARK 3 SOLVENT ATOMS : 135 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3287.7 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 29 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 31477 REMARK 3 NUMBER OF RESTRAINTS : 41831 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.108 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.074 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.084 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 3NDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000059703. 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 : 24746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 5.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 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: PDB ENTRY 3K4V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 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 31.39250 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: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 B 9 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ILE B 51 CA - C - N ANGL. DEV. = 15.1 DEGREES REMARK 500 ARG D 41 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG D 57 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG D 87 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG D 87 NE - CZ - NH2 ANGL. DEV. = -3.8 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 ILE B 51 -77.58 -49.57 REMARK 500 REMARK 500 REMARK: NULL 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 CL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA C 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS C 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROC D 100 DBREF 3NDT A 2 100 UNP P03366 POL_HV1B1 1 99 DBREF 3NDT B 2 100 UNP P03366 POL_HV1B1 1 99 DBREF 3NDT C 1 99 UNP P03366 POL_HV1B1 1 99 DBREF 3NDT D 1 99 UNP P03366 POL_HV1B1 1 99 SEQADV 3NDT ARF A 1 UNP P03366 INSERTION SEQADV 3NDT LYS A 8 UNP P03366 GLN 7 ENGINEERED MUTATION SEQADV 3NDT ILE A 34 UNP P03366 LEU 33 ENGINEERED MUTATION SEQADV 3NDT ILE A 64 UNP P03366 LEU 63 ENGINEERED MUTATION SEQADV 3NDT ALA A 68 UNP P03366 CYS 67 ENGINEERED MUTATION SEQADV 3NDT ALA A 96 UNP P03366 CYS 95 ENGINEERED MUTATION SEQADV 3NDT ARF B 1 UNP P03366 INSERTION SEQADV 3NDT LYS B 8 UNP P03366 GLN 7 ENGINEERED MUTATION SEQADV 3NDT ILE B 34 UNP P03366 LEU 33 ENGINEERED MUTATION SEQADV 3NDT ILE B 64 UNP P03366 LEU 63 ENGINEERED MUTATION SEQADV 3NDT ALA B 68 UNP P03366 CYS 67 ENGINEERED MUTATION SEQADV 3NDT ALA B 96 UNP P03366 CYS 95 ENGINEERED MUTATION SEQADV 3NDT ARF C 0 UNP P03366 INSERTION SEQADV 3NDT LYS C 7 UNP P03366 GLN 7 ENGINEERED MUTATION SEQADV 3NDT ILE C 33 UNP P03366 LEU 33 ENGINEERED MUTATION SEQADV 3NDT ILE C 63 UNP P03366 LEU 63 ENGINEERED MUTATION SEQADV 3NDT ALA C 67 UNP P03366 CYS 67 ENGINEERED MUTATION SEQADV 3NDT ALA C 95 UNP P03366 CYS 95 ENGINEERED MUTATION SEQADV 3NDT ARF D 0 UNP P03366 INSERTION SEQADV 3NDT LYS D 7 UNP P03366 GLN 7 ENGINEERED MUTATION SEQADV 3NDT ILE D 33 UNP P03366 LEU 33 ENGINEERED MUTATION SEQADV 3NDT ILE D 63 UNP P03366 LEU 63 ENGINEERED MUTATION SEQADV 3NDT ALA D 67 UNP P03366 CYS 67 ENGINEERED MUTATION SEQADV 3NDT ALA D 95 UNP P03366 CYS 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 CL A 102 1 HET DMS A 103 4 HET DMS A 104 4 HET NA B 101 1 HET CL B 102 1 HET CL B 103 1 HET CL B 104 1 HET CL B 105 1 HET CL B 106 1 HET NA C 100 1 HET CL C 101 1 HET DMS C 102 4 HET DMS C 103 4 HET ROC D 100 98 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 CL CHLORIDE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM NA SODIUM ION HETSYN ROC FORTOVASE; SAQUINAVIR; RO 31-8959 FORMUL 1 ARF 2(C H3 N O) FORMUL 5 ROC 2(C38 H50 N6 O5) FORMUL 6 CL 7(CL 1-) FORMUL 7 DMS 4(C2 H6 O S) FORMUL 9 NA 2(NA 1+) FORMUL 20 HOH *135(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 ASN A 99 O THR B 97 SHEET 4 A 4 GLN B 3 ILE B 4 -1 O ILE B 4 N LEU A 98 SHEET 1 B 8 TRP A 43 GLY A 50 0 SHEET 2 B 8 GLY A 53 ILE A 67 -1 O VAL A 57 N LYS A 46 SHEET 3 B 8 HIS A 70 VAL A 78 -1 O HIS A 70 N ILE A 67 SHEET 4 B 8 VAL A 33 ILE A 34 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 TRP B 43 GLY B 50 0 SHEET 2 C 8 GLY B 53 ILE B 67 -1 O VAL B 57 N LYS B 46 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 VAL B 12 O ALA B 23 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 VAL D 56 N LYS D 45 SHEET 3 F 8 HIS D 69 VAL D 77 -1 O VAL D 77 N ARG D 57 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 SITE 1 AC1 29 ARG A 9 ASP A 26 GLY A 28 ALA A 29 SITE 2 AC1 29 ASP A 30 ASP A 31 VAL A 33 ILE A 48 SITE 3 AC1 29 GLY A 49 GLY A 50 ILE A 51 THR A 81 SITE 4 AC1 29 PRO A 82 ILE A 85 HOH A 116 HOH A 324 SITE 5 AC1 29 ARG B 9 ASP B 26 GLY B 28 ALA B 29 SITE 6 AC1 29 ASP B 30 ASP B 31 GLY B 49 GLY B 50 SITE 7 AC1 29 ILE B 51 PRO B 82 ILE B 85 HOH B 119 SITE 8 AC1 29 TRP C 6 SITE 1 AC2 1 SER B 38 SITE 1 AC3 5 LYS A 15 GLY A 18 ILE A 64 DMS A 104 SITE 2 AC3 5 GLY B 18 SITE 1 AC4 8 GLY A 18 DMS A 103 HOH A 115 LYS B 15 SITE 2 AC4 8 ILE B 16 GLY B 17 GLY B 18 ILE B 64 SITE 1 AC5 1 LYS B 8 SITE 1 AC6 2 LYS A 15 ILE B 64 SITE 1 AC7 3 THR C 12 GLU C 65 GLY C 68 SITE 1 AC8 1 GLY D 40 SITE 1 AC9 7 GLY C 17 DMS C 103 LYS D 14 ILE D 15 SITE 2 AC9 7 GLY D 16 GLY D 17 ILE D 63 SITE 1 BC1 6 LYS C 14 ILE C 15 GLY C 16 GLY C 17 SITE 2 BC1 6 DMS C 102 GLY D 17 SITE 1 BC2 26 ARG C 8 LEU C 23 ASP C 25 GLY C 27 SITE 2 BC2 26 ALA C 28 ASP C 29 ASP C 30 GLY C 48 SITE 3 BC2 26 GLY C 49 ILE C 50 PRO C 81 ILE C 84 SITE 4 BC2 26 HOH C 107 ARG D 8 ASP D 25 GLY D 27 SITE 5 BC2 26 ALA D 28 ASP D 29 ASP D 30 GLY D 48 SITE 6 BC2 26 GLY D 49 ILE D 50 THR D 80 ILE D 84 SITE 7 BC2 26 HOH D 102 HOH D 116 CRYST1 51.294 62.785 59.171 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 0.019495 0.000000 0.002851 0.00000 SCALE2 0.000000 0.015927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017080 0.00000 HETATM 1 N ARF A 1 7.412 -5.725 39.179 1.00 52.72 N ANISOU 1 N ARF A 1 7744 7076 5211 -1468 -984 -398 N HETATM 2 C ARF A 1 7.936 -6.490 38.217 1.00 47.37 C ANISOU 2 C ARF A 1 6124 7133 4741 -52 -824 1057 C HETATM 3 O ARF A 1 8.767 -7.367 38.507 1.00 51.05 O ANISOU 3 O ARF A 1 9298 3977 6124 -888 -1175 2905 O