HEADER HYDROLASE 17-SEP-09 3JVW TITLE HIV-1 PROTEASE MUTANT G86A WITH SYMMETRIC INHIBITOR DMP323 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A, B; 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, RETROPEPSIN, PR, REVERSE COMPND 8 TRANSCRIPTASE/RIBONUCLEASE H, P66 RT, P51 RT, P15, INTEGRASE, IN; COMPND 9 EC: 3.4.23.16; COMPND 10 ENGINEERED: YES; COMPND 11 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, HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS HIV-1 PROTEASE, MUTANT G86A, SYMMETRIC INHIBITOR, DMP323, AIDS, KEYWDS 2 ASPARTYL PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TIE,I.T.WEBER REVDAT 5 06-SEP-23 3JVW 1 REMARK REVDAT 4 13-OCT-21 3JVW 1 COMPND REMARK SEQADV HETNAM REVDAT 3 01-NOV-17 3JVW 1 REMARK REVDAT 2 02-FEB-10 3JVW 1 JRNL REVDAT 1 08-DEC-09 3JVW 0 JRNL AUTH R.ISHIMA,Q.GONG,Y.TIE,I.T.WEBER,J.M.LOUIS JRNL TITL HIGHLY CONSERVED GLYCINE 86 AND ARGININE 87 RESIDUES JRNL TITL 2 CONTRIBUTE DIFFERENTLY TO THE STRUCTURE AND ACTIVITY OF THE JRNL TITL 3 MATURE HIV-1 PROTEASE JRNL REF PROTEINS V. 78 1015 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19899162 JRNL DOI 10.1002/PROT.22625 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.8 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) : 0.229 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.226 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 983 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 19742 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.209 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.205 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 812 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 15845 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1624.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6666 REMARK 3 NUMBER OF RESTRAINTS : 6440 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.032 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.083 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 3JVW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 90.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99997 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22278 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25400 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: PDB ENTRY 2IEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% DMSO,0.9M NACL,SODIUM ACETATE REMARK 280 BUFFER, PH 4.60, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 29.03350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.03350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.17900 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: DIMER 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 ARG A 57 CD - NE - CZ ANGL. DEV. = 9.8 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 DMP A 323 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IEN RELATED DB: PDB REMARK 900 WILD-TYPE HIV-1 PROTEASE WITH DARUNAVIR REMARK 900 RELATED ID: 3JW2 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE MUTANT G86S WITH DARUNAVIR REMARK 900 RELATED ID: 3JVY RELATED DB: PDB REMARK 900 HIV-1 PROTEASE MUTANT G86A WITH DARUNAVIR DBREF 3JVW A 1 99 UNP P03367 POL_HV1BR 501 599 DBREF 3JVW B 101 199 UNP P03367 POL_HV1BR 501 599 SEQADV 3JVW LYS A 7 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3JVW ILE A 33 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3JVW ILE A 63 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3JVW ALA A 67 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3JVW ALA A 86 UNP P03367 GLY 586 ENGINEERED MUTATION SEQADV 3JVW ALA A 95 UNP P03367 CYS 595 ENGINEERED MUTATION SEQADV 3JVW LYS B 107 UNP P03367 GLN 507 ENGINEERED MUTATION SEQADV 3JVW ILE B 133 UNP P03367 LEU 533 ENGINEERED MUTATION SEQADV 3JVW ILE B 163 UNP P03367 LEU 563 ENGINEERED MUTATION SEQADV 3JVW ALA B 167 UNP P03367 CYS 567 ENGINEERED MUTATION SEQADV 3JVW ALA B 186 UNP P03367 GLY 586 ENGINEERED MUTATION SEQADV 3JVW ALA B 195 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 ALA 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 ALA ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET DMP A 323 42 HETNAM DMP [4-R-(-4-ALPHA,5-ALPHA,6-BETA,7-BETA)]-HEXAHYDRO-5,6- HETNAM 2 DMP BIS(HYDROXY)-[1,3-BIS([4-HYDROXYMETHYL-PHENYL]METHYL)- HETNAM 3 DMP 4,7-BIS(PHEN YLMETHYL)]-2H-1,3-DIAZEPINONE HETSYN DMP DMP323(INHIBITOR OF DUPONT MERCK) FORMUL 3 DMP C35 H38 N2 O5 FORMUL 4 HOH *85(H2 O) HELIX 1 1 ALA A 86 THR A 91 1 6 HELIX 2 2 ALA 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 THR A 96 O ASN B 198 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 GLN A 58 N LYS A 43 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O VAL A 77 N ARG A 57 SHEET 4 B 8 THR A 31 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 VAL A 11 O ALA A 22 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 148 0 SHEET 2 C 8 PHE B 153 ILE B 166 -1 O VAL B 156 N LYS B 145 SHEET 3 C 8 HIS B 169 VAL B 177 -1 O HIS B 169 N ILE B 166 SHEET 4 C 8 VAL B 132 ILE B 133 1 N ILE B 133 O LEU B 176 SHEET 5 C 8 ASN B 183 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 ASN B 183 SHEET 7 C 8 LEU B 110 ILE B 115 -1 N ILE B 113 O LYS B 120 SHEET 8 C 8 PHE B 153 ILE B 166 -1 O GLU B 165 N LYS B 114 SITE 1 AC1 18 ASP A 25 GLY A 27 ASP A 29 ASP A 30 SITE 2 AC1 18 VAL A 32 GLY A 48 GLY A 49 ILE A 50 SITE 3 AC1 18 HOH A1033 ASP B 125 GLY B 127 ALA B 128 SITE 4 AC1 18 ASP B 129 ASP B 130 GLY B 148 GLY B 149 SITE 5 AC1 18 ILE B 150 PRO B 181 CRYST1 58.067 86.358 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 0.017221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021463 0.00000