HEADER HYDROLASE/HYDROLASE INHIBITOR 06-JUL-16 5KQY TITLE PROTEASE E35D-DRV COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE E35D-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 5KQY 1 HETSYN REVDAT 4 04-DEC-19 5KQY 1 REMARK REVDAT 3 20-SEP-17 5KQY 1 JRNL REMARK REVDAT 2 16-NOV-16 5KQY 1 JRNL REVDAT 1 21-SEP-16 5KQY 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. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28189 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 17.0675 - 3.9613 1.00 2016 154 0.1800 0.1928 REMARK 3 2 3.9613 - 3.1507 1.00 1913 146 0.1681 0.1686 REMARK 3 3 3.1507 - 2.7543 1.00 1894 145 0.1790 0.1968 REMARK 3 4 2.7543 - 2.5033 1.00 1887 143 0.1929 0.2100 REMARK 3 5 2.5033 - 2.3244 1.00 1865 143 0.1954 0.2156 REMARK 3 6 2.3244 - 2.1876 1.00 1866 143 0.1815 0.2138 REMARK 3 7 2.1876 - 2.0782 1.00 1846 140 0.1748 0.2019 REMARK 3 8 2.0782 - 1.9879 1.00 1872 141 0.1797 0.2148 REMARK 3 9 1.9879 - 1.9115 1.00 1853 142 0.1745 0.2166 REMARK 3 10 1.9115 - 1.8456 1.00 1856 142 0.1928 0.2296 REMARK 3 11 1.8456 - 1.7880 1.00 1831 140 0.1957 0.2505 REMARK 3 12 1.7880 - 1.7369 1.00 1849 141 0.2066 0.2498 REMARK 3 13 1.7369 - 1.6912 1.00 1820 140 0.2104 0.2234 REMARK 3 14 1.6912 - 1.6500 1.00 1822 139 0.2178 0.2469 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.260 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 1588 REMARK 3 ANGLE : 1.167 2155 REMARK 3 CHIRALITY : 0.066 257 REMARK 3 PLANARITY : 0.005 265 REMARK 3 DIHEDRAL : 16.918 594 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 5KQY 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_1000222242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-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 : 28265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 17.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 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 (%): 53.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.08000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.08500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.08000 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 314 O HOH B 320 2.15 REMARK 500 O HOH A 155 O HOH A 176 2.17 REMARK 500 O HOH B 218 O HOH B 283 2.17 REMARK 500 O HOH A 154 O HOH A 180 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 206 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 207 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A 208 DISTANCE = 8.67 ANGSTROMS 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: 5KQZ RELATED DB: PDB REMARK 900 RELATED ID: 5KR0 RELATED DB: PDB REMARK 900 RELATED ID: 5KR1 RELATED DB: PDB REMARK 900 RELATED ID: 5KR2 RELATED DB: PDB DBREF 5KQY A 1 99 UNP C8BD48 C8BD48_9HIV1 1 99 DBREF 5KQY B 1 99 UNP C8BD48 C8BD48_9HIV1 1 99 SEQADV 5KQY LYS A 7 UNP C8BD48 GLN 7 CONFLICT SEQADV 5KQY ASN A 25 UNP C8BD48 ASP 25 CONFLICT SEQADV 5KQY ILE A 33 UNP C8BD48 LEU 33 CONFLICT SEQADV 5KQY ILE A 63 UNP C8BD48 UNK 63 CONFLICT SEQADV 5KQY ALA A 67 UNP C8BD48 CYS 67 CONFLICT SEQADV 5KQY ALA A 95 UNP C8BD48 CYS 95 CONFLICT SEQADV 5KQY LYS B 7 UNP C8BD48 GLN 7 CONFLICT SEQADV 5KQY ASN B 25 UNP C8BD48 ASP 25 CONFLICT SEQADV 5KQY ILE B 33 UNP C8BD48 LEU 33 CONFLICT SEQADV 5KQY ILE B 63 UNP C8BD48 UNK 63 CONFLICT SEQADV 5KQY ALA B 67 UNP C8BD48 CYS 67 CONFLICT SEQADV 5KQY ALA B 95 UNP C8BD48 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 ILE 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 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 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 ILE 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 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 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 *236(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLN A 92 GLY A 94 5 3 HELIX 3 AA3 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 THR A 96 O ASN B 98 SHEET 4 AA1 4 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 AA2 8 TRP A 42 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 GLY A 78 -1 O HIS A 69 N ILE A 66 SHEET 4 AA2 8 THR A 31 GLU A 34 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 ILE 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 ILE 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 19 ASN A 25 GLY A 27 ASP A 30 ILE A 47 SITE 2 AC1 19 GLY A 48 GLY A 49 ILE A 50 PRO A 81 SITE 3 AC1 19 VAL A 82 ILE A 84 ASN B 25 GLY B 27 SITE 4 AC1 19 ALA B 28 ASP B 29 ASP B 30 GLY B 48 SITE 5 AC1 19 GLY B 49 ILE B 50 HOH B 209 CRYST1 45.580 58.170 86.160 90.00 90.00 90.00 P 2 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 0.021939 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017191 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011606 0.00000