HEADER HYDROLASE/HYDROLASE INHIBITOR 11-MAR-15 4YOA TITLE CRSYSTAL STRUCTURE HIV-1 PROTEASE MDR769 L33F COMPLEXED WITH DARUNAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV-1 PROTEASE, COMPLEX, DARUNAVIR, HYDROLASE/HYDROLASE INHIBITOR, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.KUIPER,B.KEUSCH,T.G.DEWDNEY,P.CHORDIA,J.S.BRUNZELLE,K.ROSS, AUTHOR 2 I.A.KOVARI,R.MACARTHUR,H.SALIMNIA,L.C.KOVARI REVDAT 4 27-SEP-23 4YOA 1 REMARK REVDAT 3 30-MAR-22 4YOA 1 HETSYN REVDAT 2 18-APR-18 4YOA 1 SOURCE KEYWDS JRNL REMARK REVDAT 1 08-JUL-15 4YOA 0 JRNL AUTH B.D.KUIPER,B.J.KEUSCH,T.G.DEWDNEY,P.CHORDIA,K.ROSS, JRNL AUTH 2 J.S.BRUNZELLE,I.A.KOVARI,R.MACARTHUR,H.SALIMNIA,L.C.KOVARI JRNL TITL THE L33F DARUNAVIR RESISTANCE MUTATION ACTS AS A MOLECULAR JRNL TITL 2 ANCHOR REDUCING THE FLEXIBILITY OF THE HIV-1 PROTEASE 30S JRNL TITL 3 AND 80S LOOPS. JRNL REF BIOCHEM BIOPHYS REP V. 2 160 2015 JRNL REFN ESSN 2405-5808 JRNL PMID 29124158 JRNL DOI 10.1016/J.BBREP.2015.06.003 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12478 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 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 27.2706 - 3.5285 0.99 1358 151 0.1751 0.2038 REMARK 3 2 3.5285 - 2.8016 1.00 1275 143 0.1880 0.2154 REMARK 3 3 2.8016 - 2.4477 1.00 1257 139 0.2007 0.2175 REMARK 3 4 2.4477 - 2.2240 1.00 1249 139 0.1939 0.2374 REMARK 3 5 2.2240 - 2.0647 1.00 1222 135 0.1965 0.2637 REMARK 3 6 2.0647 - 1.9430 1.00 1230 136 0.2069 0.2678 REMARK 3 7 1.9430 - 1.8457 1.00 1218 136 0.2101 0.2600 REMARK 3 8 1.8457 - 1.7654 1.00 1220 136 0.2322 0.3371 REMARK 3 9 1.7654 - 1.6974 1.00 1201 133 0.2572 0.2965 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.170 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.014 844 REMARK 3 ANGLE : 1.543 1156 REMARK 3 CHIRALITY : 0.079 138 REMARK 3 PLANARITY : 0.006 144 REMARK 3 DIHEDRAL : 18.075 326 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:99) REMARK 3 ORIGIN FOR THE GROUP (A): -2.5067 4.1052 -14.1033 REMARK 3 T TENSOR REMARK 3 T11: 0.2071 T22: 0.2082 REMARK 3 T33: 0.2117 T12: -0.0443 REMARK 3 T13: 0.0518 T23: 0.0018 REMARK 3 L TENSOR REMARK 3 L11: 1.1087 L22: 1.1569 REMARK 3 L33: 2.6510 L12: -0.3277 REMARK 3 L13: 0.1024 L23: 1.2848 REMARK 3 S TENSOR REMARK 3 S11: 0.0755 S12: -0.1128 S13: 0.1120 REMARK 3 S21: 0.1188 S22: -0.0595 S23: 0.0093 REMARK 3 S31: 0.2009 S32: -0.1883 S33: -0.0014 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 4YOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12545 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.697 REMARK 200 RESOLUTION RANGE LOW (A) : 102.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.20 REMARK 200 R MERGE FOR SHELL (I) : 0.61500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4YOB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 0.1 M MES, PH REMARK 280 6.2; 2.4M AMMONIUM SULFATE, 0.1 M MES, PH 6.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 51.11000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.73500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.55500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.73500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.73500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.66500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.73500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.55500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.73500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.66500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.11000 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: 4940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -51.11000 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 269 O HOH A 270 1.92 REMARK 500 O HOH A 229 O HOH A 239 2.05 REMARK 500 O HOH A 205 O HOH A 263 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 248 O HOH A 249 4444 1.55 REMARK 500 O HOH A 201 O HOH A 208 4454 1.87 REMARK 500 N ARG A 41 O GLY A 49 3555 2.17 REMARK 500 O HOH A 243 O HOH A 243 7555 2.19 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 017 A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YOB RELATED DB: PDB DBREF 4YOA A 1 99 UNP Q5RTL1 Q5RTL1_9HIV1 1 99 SEQADV 4YOA LYS A 7 UNP Q5RTL1 GLN 7 ENGINEERED MUTATION SEQADV 4YOA ASN A 25 UNP Q5RTL1 ASP 25 ENGINEERED MUTATION SEQADV 4YOA PHE A 33 UNP Q5RTL1 LEU 33 ENGINEERED MUTATION SEQADV 4YOA VAL A 36 UNP Q5RTL1 MET 36 ENGINEERED MUTATION SEQADV 4YOA THR A 82 UNP Q5RTL1 ALA 82 ENGINEERED MUTATION SEQADV 4YOA VAL A 84 UNP Q5RTL1 ILE 84 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO ILE VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL PHE GLU GLU VAL ASN LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS LEU ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN VAL PRO ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO THR ASN VAL ILE GLY ARG ASN LEU MET THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE HET 017 A 100 38 HETNAM 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3- HETNAM 2 017 [[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2- HETNAM 3 017 HYDROXYPROPYLCARBAMATE HETSYN 017 DARUNAVIR; TMC114; UIC-94017 FORMUL 2 017 C27 H37 N3 O7 S FORMUL 3 HOH *71(H2 O) HELIX 1 AA1 GLY A 86 GLY A 94 1 9 SHEET 1 AA1 8 LYS A 43 GLY A 48 0 SHEET 2 AA1 8 PHE A 53 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA1 8 HIS A 69 VAL A 77 -1 O VAL A 71 N ILE A 64 SHEET 4 AA1 8 VAL A 32 PHE A 33 1 N PHE A 33 O LEU A 76 SHEET 5 AA1 8 VAL A 84 ILE A 85 -1 O VAL A 84 N VAL A 32 SHEET 6 AA1 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA1 8 ILE A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA1 8 PHE A 53 ILE A 66 -1 O GLU A 65 N LYS A 14 SITE 1 AC1 9 ARG A 8 ASN A 25 GLY A 27 ALA A 28 SITE 2 AC1 9 ASP A 29 ASP A 30 VAL A 32 THR A 82 SITE 3 AC1 9 VAL A 84 CRYST1 45.470 45.470 102.220 90.00 90.00 90.00 P 41 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 0.021993 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021993 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009783 0.00000