HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JUL-16 5KR1 TITLE PROTEASE PR5-DRV COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE PR5-DRV; COMPND 3 CHAIN: A, B; 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 K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS HIV-1 PROTEASE, E35D, SALT-BRIDGE INTERACTION, NATURAL POLYMORPHISM, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.LIU,K.M.POOLE,B.P.MAHON,R.MCKENNA,G.E.FANUCCI REVDAT 5 06-MAR-24 5KR1 1 HETSYN REVDAT 4 04-DEC-19 5KR1 1 REMARK REVDAT 3 20-SEP-17 5KR1 1 JRNL REMARK REVDAT 2 16-NOV-16 5KR1 1 JRNL REVDAT 1 21-SEP-16 5KR1 0 JRNL AUTH Z.LIU,X.HUANG,L.HU,L.PHAM,K.M.POOLE,Y.TANG,B.P.MAHON,W.TANG, JRNL AUTH 2 K.LI,N.E.GOLDFARB,B.M.DUNN,R.MCKENNA,G.E.FANUCCI JRNL TITL EFFECTS OF HINGE-REGION NATURAL POLYMORPHISMS ON HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS-TYPE 1 PROTEASE STRUCTURE, DYNAMICS, JRNL TITL 3 AND DRUG PRESSURE EVOLUTION. JRNL REF J.BIOL.CHEM. V. 291 22741 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27576689 JRNL DOI 10.1074/JBC.M116.747568 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2001 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 19.1426 - 3.8466 1.00 1743 153 0.1943 0.2115 REMARK 3 2 3.8466 - 3.0572 1.00 1677 142 0.1756 0.2292 REMARK 3 3 3.0572 - 2.6719 1.00 1625 147 0.1888 0.2088 REMARK 3 4 2.6719 - 2.4281 1.00 1625 141 0.1881 0.2098 REMARK 3 5 2.4281 - 2.2544 1.00 1648 150 0.1822 0.2234 REMARK 3 6 2.2544 - 2.1216 1.00 1616 139 0.1738 0.2230 REMARK 3 7 2.1216 - 2.0155 1.00 1615 139 0.1701 0.2148 REMARK 3 8 2.0155 - 1.9279 1.00 1601 144 0.1738 0.2002 REMARK 3 9 1.9279 - 1.8537 1.00 1627 134 0.1816 0.2158 REMARK 3 10 1.8537 - 1.7898 1.00 1594 151 0.1924 0.2203 REMARK 3 11 1.7898 - 1.7339 1.00 1598 139 0.1871 0.2223 REMARK 3 12 1.7339 - 1.6843 1.00 1606 139 0.1961 0.2332 REMARK 3 13 1.6843 - 1.6400 1.00 1595 137 0.2296 0.2553 REMARK 3 14 1.6400 - 1.6000 1.00 1572 146 0.2819 0.2962 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 20.080 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 : 0.007 1584 REMARK 3 ANGLE : 1.155 2151 REMARK 3 CHIRALITY : 0.045 257 REMARK 3 PLANARITY : 0.006 264 REMARK 3 DIHEDRAL : 13.610 592 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5KR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222256. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.1.1 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 21.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.090 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 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: NULL REMARK 200 SOFTWARE USED: PHASER 2.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.48000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.86500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.86500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.48000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.00000 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 B 250 O HOH B 287 2.07 REMARK 500 O HOH B 285 O HOH B 291 2.12 REMARK 500 O HOH A 182 O HOH A 192 2.12 REMARK 500 O HOH A 177 O HOH A 193 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 017 B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KQX RELATED DB: PDB REMARK 900 RELATED ID: 5KQY RELATED DB: PDB REMARK 900 RELATED ID: 5KQZ RELATED DB: PDB REMARK 900 RELATED ID: 5KR0 RELATED DB: PDB REMARK 900 RELATED ID: 5KR1 RELATED DB: PDB DBREF 5KR1 A 1 99 UNP V5YAB1 V5YAB1_9HIV1 1 99 DBREF 5KR1 B 1 99 UNP V5YAB1 V5YAB1_9HIV1 1 99 SEQADV 5KR1 LYS A 7 UNP V5YAB1 GLN 7 CONFLICT SEQADV 5KR1 ASN A 25 UNP V5YAB1 ASP 25 CONFLICT SEQADV 5KR1 ILE A 33 UNP V5YAB1 LEU 33 CONFLICT SEQADV 5KR1 LYS A 57 UNP V5YAB1 ARG 57 CONFLICT SEQADV 5KR1 ILE A 63 UNP V5YAB1 THR 63 CONFLICT SEQADV 5KR1 ALA A 67 UNP V5YAB1 CYS 67 CONFLICT SEQADV 5KR1 ALA A 95 UNP V5YAB1 CYS 95 CONFLICT SEQADV 5KR1 LYS B 7 UNP V5YAB1 GLN 7 CONFLICT SEQADV 5KR1 ASN B 25 UNP V5YAB1 ASP 25 CONFLICT SEQADV 5KR1 ILE B 33 UNP V5YAB1 LEU 33 CONFLICT SEQADV 5KR1 LYS B 57 UNP V5YAB1 ARG 57 CONFLICT SEQADV 5KR1 ILE B 63 UNP V5YAB1 THR 63 CONFLICT SEQADV 5KR1 ALA B 67 UNP V5YAB1 CYS 67 CONFLICT SEQADV 5KR1 ALA B 95 UNP V5YAB1 CYS 95 CONFLICT SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU ASP MET ASN LEU PRO SEQRES 4 A 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL LYS 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 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 VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE GLU ASP MET ASN LEU PRO SEQRES 4 B 99 GLY LYS TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL LYS 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 GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET 017 B 101 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 3 017 C27 H37 N3 O7 S FORMUL 4 HOH *206(H2 O) HELIX 1 AA1 GLY A 86 ILE A 93 1 8 HELIX 2 AA2 GLY B 86 THR B 91 1 6 SHEET 1 AA1 4 GLN A 2 ILE A 3 0 SHEET 2 AA1 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 AA1 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 AA1 4 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 AA2 8 LYS A 43 GLY A 49 0 SHEET 2 AA2 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA2 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 AA2 8 THR A 31 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 AA2 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 AA2 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA2 8 LEU A 10 VAL A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA2 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 AA3 8 LYS B 43 GLY B 49 0 SHEET 2 AA3 8 GLY B 52 ILE B 66 -1 O GLN B 58 N LYS B 43 SHEET 3 AA3 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 SHEET 4 AA3 8 VAL B 32 ILE B 33 1 N ILE B 33 O LEU B 76 SHEET 5 AA3 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 AA3 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 AA3 8 LEU B 10 VAL B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 AA3 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SITE 1 AC1 16 ASN A 25 GLY A 27 ALA A 28 ILE A 47 SITE 2 AC1 16 GLY A 48 GLY A 49 ILE A 84 ASN B 25 SITE 3 AC1 16 GLY B 27 ALA B 28 ASP B 29 ASP B 30 SITE 4 AC1 16 GLY B 48 ILE B 50 HOH B 219 HOH B 257 CRYST1 50.960 58.000 61.730 90.00 90.00 90.00 P 21 21 21 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 0.019623 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016200 0.00000