HEADER HYDROLASE/INHIBITOR 28-APR-05 2BQV TITLE HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR AHA455 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPLEX WITH INHIBITOR AHA455 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 VARIANT: D10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11D KEYWDS HYDROLASE/INHIBITOR, HYDROLASE-INHIBITOR COMPLEX, HIV-1 PROTEASE, KEYWDS 2 INHIBITOR, DRUG DESIGN, HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.UNGE,J.K.EKEGREN,H.V.SCHENK,M.ZREIK SAFA,H.WALLBERG,B.SAMUELSSON, AUTHOR 2 A.HALLBERG REVDAT 4 13-DEC-23 2BQV 1 REMARK REVDAT 3 17-JAN-18 2BQV 1 REMARK REVDAT 2 24-FEB-09 2BQV 1 VERSN REVDAT 1 14-DEC-05 2BQV 0 JRNL AUTH J.K.EKEGREN,T.UNGE,M.Z.SAFA,H.WALLBERG,B.SAMUELSSON, JRNL AUTH 2 A.HALLBERG JRNL TITL A NEW CLASS OF HIV-1 PROTEASE INHIBITORS CONTAINING A JRNL TITL 2 TERTIARY ALCOHOL IN THE TRANSITION-STATE MIMICKING SCAFFOLD. JRNL REF J.MED.CHEM. V. 48 8098 2005 JRNL REFN ISSN 0022-2623 JRNL PMID 16335934 JRNL DOI 10.1021/JM050790T REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 62.0 REMARK 3 NUMBER OF REFLECTIONS : 14686 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 SET) : 0.206 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 740 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.07200 REMARK 3 B22 (A**2) : 3.14800 REMARK 3 B33 (A**2) : 1.92400 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.264 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 41.74 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : AHA_PAR.TXT REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : AHA_TOP.TXT REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023803. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 287.0 REMARK 200 PH : 5.50 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.079 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14691 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.0 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.24000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1D4J REMARK 200 REMARK 200 REMARK: RIGID BODY AND REFINE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.50 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 30.04100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.72600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.04100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.72600 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 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: PQS 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: 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 PRO B 179 61.68 -68.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A1A A1100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HVC RELATED DB: PDB REMARK 900 HIV-1 PROTEASE (TETHERED DIMER LINKED BY GLY-GLY-SER-SER-GLY) REMARK 900 COMPLEXED WITH A- 76928 REMARK 900 RELATED ID: 2BB9 RELATED DB: PDB REMARK 900 STRUCTURE OF HIV1 PROTEASE AND AKC4P_133A COMPLEX. DBREF 2BQV A 1 99 UNP O92139 O92139_9HIV1 1 99 DBREF 2BQV B 101 199 UNP O92139 O92139_9HIV1 1 99 SEQRES 1 A 99 PRO GLN ILE THR LEU TRP GLN 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 LEU 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 LEU ILE GLU SEQRES 6 A 99 ILE CYS 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 CYS THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP GLN 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 LEU 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 LEU ILE GLU SEQRES 6 B 99 ILE CYS 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 CYS THR LEU ASN PHE HET A1A A1100 43 HETNAM A1A 6-AMINO HEXANOIC ACID FORMUL 3 A1A C33 H40 N4 O6 FORMUL 4 HOH *47(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 186 THR B 191 1 6 SHEET 1 AA 4 GLN A 2 ILE A 3 0 SHEET 2 AA 4 THR B 196 ASN B 198 -1 O LEU B 197 N ILE A 3 SHEET 3 AA 4 THR A 96 ASN A 98 -1 O THR A 96 N ASN B 198 SHEET 4 AA 4 GLN B 102 ILE B 103 -1 O ILE B 103 N LEU A 97 SHEET 1 AB 8 LEU A 10 ILE A 15 0 SHEET 2 AB 8 GLN A 18 LEU A 24 -1 O GLN A 18 N ILE A 15 SHEET 3 AB 8 ILE A 84 ILE A 85 1 N ILE A 85 O LEU A 23 SHEET 4 AB 8 VAL A 32 LEU A 33 -1 O VAL A 32 N ILE A 84 SHEET 5 AB 8 HIS A 69 VAL A 77 1 O LEU A 76 N LEU A 33 SHEET 6 AB 8 GLY A 52 ILE A 66 -1 O ARG A 57 N VAL A 77 SHEET 7 AB 8 LEU A 10 ILE A 15 -1 O LYS A 14 N GLU A 65 SHEET 8 AB 8 LEU A 10 ILE A 15 0 SHEET 1 BA 8 LEU B 110 ILE B 115 0 SHEET 2 BA 8 GLN B 118 LEU B 124 -1 O GLN B 118 N ILE B 115 SHEET 3 BA 8 ILE B 184 ILE B 185 1 N ILE B 185 O LEU B 123 SHEET 4 BA 8 VAL B 132 LEU B 133 -1 O VAL B 132 N ILE B 184 SHEET 5 BA 8 HIS B 169 VAL B 177 1 O LEU B 176 N LEU B 133 SHEET 6 BA 8 GLY B 152 ILE B 166 -1 O ARG B 157 N VAL B 177 SHEET 7 BA 8 LEU B 110 ILE B 115 -1 O LYS B 114 N GLU B 165 SHEET 8 BA 8 LEU B 110 ILE B 115 0 SITE 1 AC1 19 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC1 19 ASP A 29 ASP A 30 VAL A 32 GLY A 48 SITE 3 AC1 19 GLY A 49 VAL A 82 HOH A2021 ASP B 125 SITE 4 AC1 19 GLY B 127 ALA B 128 ASP B 129 GLY B 148 SITE 5 AC1 19 GLY B 149 ILE B 150 VAL B 182 CRYST1 60.082 87.452 47.124 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 0.016644 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011435 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021221 0.00000