HEADER HYDROLASE/HYDROLASE INHIBITOR 04-DEC-12 4I8Z TITLE CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH NON- TITLE 2 PEPTIDIC INHIBITOR, GRL008 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV-1 PROTEASE, HIV-1 PROTEASE-INHIBITOR COMPLEX, HYDROLASE, GRL008, KEYWDS 2 NON-PEPTIDIC INHIBITOR, PROTEASE INHIBITOR, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.S.YEDIDI,I.PALMER,D.DAS,P.T.WINGFIELD,A.K.GHOSH,H.MITSUYA REVDAT 3 28-FEB-24 4I8Z 1 REMARK REVDAT 2 25-SEP-13 4I8Z 1 JRNL REVDAT 1 24-JUL-13 4I8Z 0 JRNL AUTH R.S.YEDIDI,K.MAEDA,W.S.FYVIE,M.STEFFEY,D.A.DAVIS,I.PALMER, JRNL AUTH 2 M.AOKI,J.D.KAUFMAN,S.J.STAHL,H.GARIMELLA,D.DAS, JRNL AUTH 3 P.T.WINGFIELD,A.K.GHOSH,H.MITSUYA JRNL TITL P2' BENZENE CARBOXYLIC ACID MOIETY IS ASSOCIATED WITH JRNL TITL 2 DECREASE IN CELLULAR UPTAKE: EVALUATION OF NOVEL JRNL TITL 3 NON-PEPTIDIC HIV-1 PROTEASE INHIBITORS CONTAINING P2 JRNL TITL 4 BIS-TETRAHYDROFURAN MOIETY. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 57 4920 2013 JRNL REFN ISSN 0066-4804 JRNL PMID 23877703 JRNL DOI 10.1128/AAC.00868-13 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17967 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 915 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.0385 - 3.3464 0.99 2482 128 0.1523 0.1727 REMARK 3 2 3.3464 - 2.6567 1.00 2446 135 0.1881 0.2607 REMARK 3 3 2.6567 - 2.3210 1.00 2412 144 0.2051 0.2646 REMARK 3 4 2.3210 - 2.1089 1.00 2429 132 0.1933 0.2059 REMARK 3 5 2.1089 - 1.9578 0.99 2439 121 0.1934 0.2319 REMARK 3 6 1.9578 - 1.8424 0.99 2427 135 0.2116 0.2465 REMARK 3 7 1.8424 - 1.7501 0.99 2417 120 0.2411 0.3025 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 51.25 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.020 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) : 0.44460 REMARK 3 B22 (A**2) : 0.44460 REMARK 3 B33 (A**2) : -0.88920 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 1628 REMARK 3 ANGLE : 1.927 2212 REMARK 3 CHIRALITY : 0.144 260 REMARK 3 PLANARITY : 0.010 268 REMARK 3 DIHEDRAL : 15.540 638 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -22.7883 0.0016 -0.2857 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.1062 REMARK 3 T33: 0.1543 T12: 0.0001 REMARK 3 T13: -0.0009 T23: 0.0347 REMARK 3 L TENSOR REMARK 3 L11: 1.6989 L22: 4.2663 REMARK 3 L33: 3.1816 L12: -0.0092 REMARK 3 L13: 0.0121 L23: 2.8507 REMARK 3 S TENSOR REMARK 3 S11: -0.0007 S12: -0.0116 S13: 0.0072 REMARK 3 S21: 0.0264 S22: 0.1055 S23: -0.1838 REMARK 3 S31: 0.0293 S32: 0.1220 S33: -0.0480 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4I8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 32.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07500 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE (PRECIPITANT) REMARK 280 IN 0.1 M BICINE BUFFER, PH 9.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.24667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.49333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.87000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.11667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.62333 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 249 O HOH A 250 1.84 REMARK 500 O HOH A 226 O HOH A 235 1.96 REMARK 500 O HOH B 142 O HOH B 160 1.97 REMARK 500 O HOH A 258 O HOH A 259 2.00 REMARK 500 SG CYS A 67 O HOH A 246 2.09 REMARK 500 NZ LYS B 45 O HOH B 150 2.13 REMARK 500 OD1 ASP A 30 O HOH A 252 2.17 REMARK 500 O ILE B 50 O HOH B 147 2.18 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 G08 A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I8W RELATED DB: PDB REMARK 900 RELATED ID: 4HLA RELATED DB: PDB DBREF 4I8Z A 1 99 UNP P0C6F2 POL_HV1LW 489 587 DBREF 4I8Z B 1 99 UNP P0C6F2 POL_HV1LW 489 587 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 G08 A 101 80 HETNAM G08 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(2S,3R)-4- HETNAM 2 G08 {[(4-CARBAMOYLPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}- HETNAM 3 G08 3-HYDROXY-1-PHENYLBUTAN-2-YL]CARBAMATE FORMUL 3 G08 C28 H37 N3 O8 S FORMUL 4 HOH *128(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 HELIX 3 3 GLN B 92 GLY B 94 5 3 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 A 4 GLN B 2 ILE B 3 -1 O ILE B 3 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 HIS A 69 N ILE A 66 SHEET 4 B 8 THR A 31 LEU A 33 1 N LEU 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 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O GLY B 52 N GLY B 49 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O ALA B 71 N ILE B 64 SHEET 4 C 8 THR B 31 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 C 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 C 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 C 8 LEU B 10 ILE B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SITE 1 AC1 27 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 27 ASP A 30 ILE A 47 GLY A 48 GLY A 49 SITE 3 AC1 27 ILE A 50 PRO A 81 VAL A 82 ILE A 84 SITE 4 AC1 27 HOH A 225 HOH A 239 LEU B 23 ASP B 25 SITE 5 AC1 27 GLY B 27 ALA B 28 ASP B 29 ASP B 30 SITE 6 AC1 27 ILE B 47 GLY B 48 GLY B 49 ILE B 50 SITE 7 AC1 27 PRO B 81 VAL B 82 ILE B 84 CRYST1 62.120 62.120 81.740 90.00 90.00 120.00 P 61 12 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 0.016098 0.009294 0.000000 0.00000 SCALE2 0.000000 0.018588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012234 0.00000