HEADER HYDROLASE/HYDROLASE INHIBITOR 17-APR-14 4Q5M TITLE D30N TETHERED HIV-1 PROTEASE DIMER/SAQUINAVIR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: CHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY COMPND 8 (NUMBERED A100 TO A104) THAT COVALENTLY LINK SUB-UNIT A WITH SUB-UNIT COMPND 9 B IN THE TETHERED DIMER. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11706; SOURCE 5 STRAIN: GROUP M SUBTYPE B (ISOLATE HXB2); SOURCE 6 GENE: GAG-POL; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.PRASHAR,S.C.BIHANI,J.L.FERRER,M.V.HOSUR REVDAT 4 08-NOV-23 4Q5M 1 REMARK REVDAT 3 24-AUG-22 4Q5M 1 COMPND JRNL REMARK SEQADV REVDAT 3 2 1 HETNAM HETSYN REVDAT 2 23-AUG-17 4Q5M 1 SOURCE REVDAT 1 08-APR-15 4Q5M 0 JRNL AUTH V.PRASHAR,S.C.BIHANI,J.L.FERRER,M.V.HOSUR JRNL TITL STRUCTURAL BASIS OF WHY NELFINAVIR-RESISTANT D30N MUTANT OF JRNL TITL 2 HIV-1 PROTEASE REMAINS SUSCEPTIBLE TO SAQUINAVIR. JRNL REF CHEM.BIOL.DRUG DES. V. 86 302 2015 JRNL REFN ESSN 1747-0285 JRNL PMID 25487655 JRNL DOI 10.1111/CBDD.12494 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 17148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 858 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 45.4405 - 3.2613 0.99 2736 145 0.1777 0.1998 REMARK 3 2 3.2613 - 2.5887 1.00 2735 144 0.2162 0.2240 REMARK 3 3 2.5887 - 2.2615 0.99 2727 143 0.2191 0.2444 REMARK 3 4 2.2615 - 2.0547 0.99 2709 143 0.2236 0.2780 REMARK 3 5 2.0547 - 1.9074 0.99 2705 142 0.2318 0.2907 REMARK 3 6 1.9074 - 1.7950 0.98 2678 141 0.2676 0.3374 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.560 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 1665 REMARK 3 ANGLE : 1.095 2267 REMARK 3 CHIRALITY : 0.069 270 REMARK 3 PLANARITY : 0.005 276 REMARK 3 DIHEDRAL : 13.573 635 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 4Q5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.934 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 45.426 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1LV1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1-5% SATURATED AMMONIUM SULFATE, REMARK 280 200/100MM PHOSPHATE/CITRATE BUFFER, 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 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 27.49667 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 54.99333 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 41.24500 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 68.74167 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 13.74833 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 100 REMARK 465 GLY A 101 REMARK 465 SER A 102 REMARK 465 SER A 103 REMARK 465 GLY A 104 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- REMARK 630 BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3- REMARK 630 HYDROXY-1 -PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO) REMARK 630 BUTANEDIAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 ROC A 1101 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: QNC ASN HP0 NTB REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ROC A 1101 REMARK 999 REMARK 999 SEQUENCE REMARK 999 CHIMERA PROTEIN WITH LINKER GLY-GLY-SER-SER-GLY (NUMBERED A100 TO REMARK 999 A104) THAT COVALENTLY LINK SUB-UNIT A WITH SUB-UNIT B IN THE REMARK 999 TETHERED DIMER. DBREF 4Q5M A 1 99 UNP P04585 POL_HV1H2 489 587 DBREF 4Q5M A 1001 1099 UNP P04585 POL_HV1H2 489 587 SEQADV 4Q5M ASN A 30 UNP P04585 ASP 518 ENGINEERED MUTATION SEQADV 4Q5M MET A 95 UNP P04585 CYS 583 ENGINEERED MUTATION SEQADV 4Q5M GLY A 100 UNP P04585 LINKER SEQADV 4Q5M GLY A 101 UNP P04585 LINKER SEQADV 4Q5M SER A 102 UNP P04585 LINKER SEQADV 4Q5M SER A 103 UNP P04585 LINKER SEQADV 4Q5M GLY A 104 UNP P04585 LINKER SEQADV 4Q5M ASN A 1030 UNP P04585 ASP 518 ENGINEERED MUTATION SEQADV 4Q5M ALA A 1095 UNP P04585 CYS 583 ENGINEERED MUTATION SEQRES 1 A 203 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 A 203 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 203 GLY ALA ASP ASN THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 A 203 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 6 A 203 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 203 GLN ILE GLY MET THR LEU ASN PHE GLY GLY SER SER GLY SEQRES 9 A 203 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 10 A 203 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 11 A 203 GLY ALA ASP ASN THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 12 A 203 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 13 A 203 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE LEU ILE GLU SEQRES 14 A 203 ILE CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 15 A 203 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 16 A 203 GLN ILE GLY ALA THR LEU ASN PHE HET ROC A1101 98 HETNAM ROC (2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT- HETNAM 2 ROC BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H- HETNAM 3 ROC ISOQUINOLIN-2-YL]-3-HYDROXY-1 -PHENYL-BUTAN-2-YL]-2- HETNAM 4 ROC (QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE HETSYN ROC FORTOVASE; SAQUINAVIR; RO 31-8959 FORMUL 2 ROC C38 H50 N6 O5 FORMUL 3 HOH *93(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLN A 92 GLY A 94 5 3 HELIX 3 3 GLY A 1086 THR A 1091 1 6 HELIX 4 4 GLN A 1092 GLY A 1094 5 3 SHEET 1 A 3 GLN A 2 VAL A 3 0 SHEET 2 A 3 THR A1096 ASN A1098 -1 O LEU A1097 N VAL A 3 SHEET 3 A 3 THR A 96 ASN A 98 -1 N ASN A 98 O THR A1096 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 VAL A 32 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 A1043 GLY A1049 0 SHEET 2 C 8 GLY A1052 ILE A1066 -1 O VAL A1056 N LYS A1045 SHEET 3 C 8 HIS A1069 VAL A1077 -1 O HIS A1069 N ILE A1066 SHEET 4 C 8 VAL A1032 LEU A1033 1 N LEU A1033 O LEU A1076 SHEET 5 C 8 ILE A1084 ILE A1085 -1 O ILE A1084 N VAL A1032 SHEET 6 C 8 GLN A1018 LEU A1024 1 N LEU A1023 O ILE A1085 SHEET 7 C 8 LEU A1010 ILE A1015 -1 N ILE A1013 O LYS A1020 SHEET 8 C 8 GLY A1052 ILE A1066 -1 O GLU A1065 N LYS A1014 SITE 1 AC1 26 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC1 26 ASP A 29 ASN A 30 GLY A 48 GLY A 49 SITE 3 AC1 26 ILE A 50 THR A 80 PRO A 81 VAL A 82 SITE 4 AC1 26 ILE A 84 ARG A1008 ASP A1025 GLY A1027 SITE 5 AC1 26 ALA A1028 ASP A1029 ASN A1030 GLY A1048 SITE 6 AC1 26 GLY A1049 ILE A1050 PRO A1081 VAL A1082 SITE 7 AC1 26 ILE A1084 HOH A1201 CRYST1 62.840 62.840 82.490 90.00 90.00 120.00 P 61 6 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 0.015913 0.009188 0.000000 0.00000 SCALE2 0.000000 0.018375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012123 0.00000