HEADER HYDROLASE 14-FEB-04 1SDV TITLE CRYSTAL STRUCTURES OF HIV PROTEASE V82A AND L90M MUTANTS REVEAL TITLE 2 CHANGES IN INDINAVIR BINDING SITE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE RETROPEPSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HIV-1 PROTEASE; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: COMPLEXED WITH INDINAVIR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG-POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DRUG RESISTANCE; HIV-1 PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.MAHALINGAM,Y.-F.WANG,P.I.BOROSS,J.TOZSER,J.M.LOUIS,R.W.HARRISON, AUTHOR 2 I.T.WEBER REVDAT 3 23-AUG-23 1SDV 1 REMARK SEQADV REVDAT 2 24-FEB-09 1SDV 1 VERSN REVDAT 1 25-MAY-04 1SDV 0 JRNL AUTH B.MAHALINGAM,Y.-F.WANG,P.I.BOROSS,J.TOZSER,J.M.LOUIS, JRNL AUTH 2 R.W.HARRISON,I.T.WEBER JRNL TITL CRYSTAL STRUCTURES OF HIV PROTEASE V82A AND L90M MUTANTS JRNL TITL 2 REVEAL CHANGES IN THE INDINAVIR-BINDING SITE JRNL REF EUR.J.BIOCHEM. V. 271 1516 2004 JRNL REFN ISSN 0014-2956 JRNL PMID 15066177 JRNL DOI 10.1111/J.1432-1033.2004.04060.X REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 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) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.160 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2074 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 41492 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.150 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.150 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1872 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 37584 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1508 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1738.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1627.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15701 REMARK 3 NUMBER OF RESTRAINTS : 19180 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.028 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.055 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.066 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.043 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.034 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.070 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 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 1SDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97903 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.7 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 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: AMORE REMARK 200 STARTING MODEL: 1DAZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CITRATE/PHOSPHATE BUFFER, NACL , PH REMARK 280 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 42.91000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.36300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.91000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.36300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: SUBUNITS A AND B FORM A HOMODIMER IN THE ASYMMETRIC UNIT 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: 5320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 ASP A 29 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 41 CD - NE - CZ ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 57 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 TRP B 142 C - N - CA ANGL. DEV. = 19.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MK1 B 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FF0 RELATED DB: PDB REMARK 900 THIS ENTRY HAS THE SAME MUTATIONS AS 1FF0 ENTRY TO STABILIZE IT REMARK 900 FROM AUTOPROTEOLYSIS REMARK 900 RELATED ID: 1SDT RELATED DB: PDB REMARK 900 RELATED ID: 1SDU RELATED DB: PDB DBREF 1SDV A 1 99 UNP P03367 POL_HV1BR 69 167 DBREF 1SDV B 101 199 UNP P03367 POL_HV1BR 69 167 SEQADV 1SDV LYS A 7 UNP P03367 GLN 75 VARIANT SEQADV 1SDV ILE A 33 UNP P03367 LEU 101 VARIANT SEQADV 1SDV ILE A 63 UNP P03367 LEU 131 VARIANT SEQADV 1SDV ALA A 67 UNP P03367 CYS 135 VARIANT SEQADV 1SDV ALA A 82 UNP P03367 VAL 150 VARIANT SEQADV 1SDV ALA A 95 UNP P03367 CYS 163 VARIANT SEQADV 1SDV LYS B 107 UNP P03367 GLN 75 VARIANT SEQADV 1SDV ILE B 133 UNP P03367 LEU 101 VARIANT SEQADV 1SDV ILE B 163 UNP P03367 LEU 131 VARIANT SEQADV 1SDV ALA B 167 UNP P03367 CYS 135 VARIANT SEQADV 1SDV ALA B 182 UNP P03367 VAL 150 VARIANT SEQADV 1SDV ALA B 195 UNP P03367 CYS 163 VARIANT 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 ALA 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 ALA ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET CL A 501 1 HET CL B 500 1 HET MK1 B 902 45 HETNAM CL CHLORIDE ION HETNAM MK1 N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY HETNAM 2 MK1 BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]- HETNAM 3 MK1 4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE HETSYN MK1 INDINAVIR FORMUL 3 CL 2(CL 1-) FORMUL 5 MK1 C36 H47 N5 O4 FORMUL 6 HOH *183(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 186 ILE B 193 1 8 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 196 ASN B 198 -1 O LEU B 197 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 196 SHEET 4 A 4 GLN B 102 ILE B 103 -1 O ILE B 103 N LEU A 97 SHEET 1 B 8 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLY A 52 N GLY A 49 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O ALA A 71 N ILE A 64 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 143 GLY B 149 0 SHEET 2 C 8 GLY B 152 ILE B 166 -1 O GLN B 158 N LYS B 143 SHEET 3 C 8 HIS B 169 VAL B 177 -1 O VAL B 177 N ARG B 157 SHEET 4 C 8 VAL B 132 ILE B 133 1 N ILE B 133 O LEU B 176 SHEET 5 C 8 ILE B 184 ILE B 185 -1 O ILE B 184 N VAL B 132 SHEET 6 C 8 GLN B 118 LEU B 124 1 N LEU B 123 O ILE B 185 SHEET 7 C 8 LEU B 110 ILE B 115 -1 N ILE B 113 O LYS B 120 SHEET 8 C 8 GLY B 152 ILE B 166 -1 O GLU B 165 N LYS B 114 SITE 1 AC1 1 TRP B 106 SITE 1 AC2 4 THR A 74 ASN A 88 HOH A 357 ARG B 141 SITE 1 AC3 15 LEU A 23 ASP A 25 GLY A 27 GLY A 48 SITE 2 AC3 15 GLY A 49 ILE A 84 ASP B 125 GLY B 127 SITE 3 AC3 15 ALA B 128 ASP B 129 ASP B 130 GLY B 148 SITE 4 AC3 15 GLY B 149 PRO B 181 HOH B 316 CRYST1 85.820 58.726 46.592 90.00 90.00 90.00 P 21 21 2 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 0.011652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021463 0.00000