HEADER HYDROLASE 31-AUG-19 6KU8 TITLE STRUCTURE OF HRV-C 3C PROTEIN WITH RUPINTRIVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHINOVIRUS C; SOURCE 3 ORGANISM_TAXID: 463676; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS HRV, 3C, PROTEASE, RUPINTRIVIR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHU,S.YUAN REVDAT 3 22-NOV-23 6KU8 1 REMARK REVDAT 2 16-SEP-20 6KU8 1 JRNL REVDAT 1 25-MAR-20 6KU8 0 JRNL AUTH S.YUAN,K.FAN,Z.CHEN,Y.SUN,H.HOU,L.ZHU JRNL TITL STRUCTURE OF THE HRV-C 3C-RUPINTRIVIR COMPLEX PROVIDES NEW JRNL TITL 2 INSIGHTS FOR INHIBITOR DESIGN. JRNL REF VIROL SIN V. 35 445 2020 JRNL REFN ISSN 1995-820X JRNL PMID 32103448 JRNL DOI 10.1007/S12250-020-00196-4 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.11 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 14812 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 746 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 2.2100 - 2.0500 0.00 0 0 0.1859 0.2330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6KU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013675. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 293.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16114 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26300 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: PHASER V1.11 REMARK 200 STARTING MODEL: 3ZV8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M CITRIC ACID, 0.05 M BIS-TRIS REMARK 280 PROPANE, PH 5.0, 16% (W/V) POLYETHYLENE GLYCOL 3,350., BATCH REMARK 280 MODE, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.42650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.42650 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.45150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.81300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.45150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.81300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.42650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.45150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.81300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.42650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.45150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.81300 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 4 CG ND1 CD2 CE1 NE2 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 603 O HOH A 733 1.94 REMARK 500 OE2 GLU A 42 O HOH A 601 2.08 REMARK 500 F1 AG7 A 501 O HOH A 606 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 32 -125.88 48.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 AG7 A 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AG7 A 501 DBREF 6KU8 A 4 180 UNP E5D8F2 E5D8F2_9ENTO 1514 1690 SEQADV 6KU8 HIS A -2 UNP E5D8F2 EXPRESSION TAG SEQADV 6KU8 HIS A -1 UNP E5D8F2 EXPRESSION TAG SEQADV 6KU8 HIS A 0 UNP E5D8F2 EXPRESSION TAG SEQADV 6KU8 HIS A 1 UNP E5D8F2 EXPRESSION TAG SEQADV 6KU8 HIS A 2 UNP E5D8F2 EXPRESSION TAG SEQADV 6KU8 HIS A 3 UNP E5D8F2 EXPRESSION TAG SEQRES 1 A 183 HIS HIS HIS HIS HIS HIS HIS GLU PHE VAL ARG ALA LEU SEQRES 2 A 183 ILE LYS ARG ASN CYS HIS VAL ILE THR THR SER LYS GLY SEQRES 3 A 183 GLU PHE ASN MET LEU GLY ILE HIS ASP ASN CYS ALA VAL SEQRES 4 A 183 VAL PRO THR HIS ALA GLU CYS GLY ASP SER VAL THR ILE SEQRES 5 A 183 ASP GLY ARG GLU VAL ARG VAL LEU LYS GLN CYS ILE LEU SEQRES 6 A 183 THR ASP THR ASN ASP THR ASP THR GLU ILE THR LEU LEU SEQRES 7 A 183 TRP LEU ASP GLN ASN GLU LYS PHE ARG ASP ILE ARG ARG SEQRES 8 A 183 PHE ILE PRO GLU HIS GLN ARG GLU TRP SER ASN MET HIS SEQRES 9 A 183 LEU ALA THR ASN VAL THR LYS PHE PRO MET LEU ASP VAL SEQRES 10 A 183 GLU VAL GLY THR VAL ILE PRO TYR GLY GLU VAL ASN LEU SEQRES 11 A 183 SER GLY ASN PRO THR CYS ARG LEU LEU LYS TYR ASN TYR SEQRES 12 A 183 PRO THR LYS PRO GLY GLN CYS GLY GLY VAL ILE ALA ASN SEQRES 13 A 183 THR GLY ASN ILE VAL ALA ILE HIS VAL GLY GLY ASN GLY SEQRES 14 A 183 ARG VAL GLY TYR GLY ALA ALA LEU LEU ARG LYS TYR PHE SEQRES 15 A 183 ALA HET AG7 A 501 74 HETNAM AG7 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE- HETNAM 2 AG7 3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO- HETNAM 3 AG7 PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER HETSYN AG7 RUPINTRIVIR, BOUND FORM FORMUL 2 AG7 C31 H41 F N4 O7 FORMUL 3 HOH *140(H2 O) HELIX 1 AA1 HIS A 4 ASN A 14 1 11 HELIX 2 AA2 HIS A 40 GLU A 42 5 3 HELIX 3 AA3 ILE A 86 ILE A 90 5 5 HELIX 4 AA4 LEU A 175 ALA A 180 5 6 SHEET 1 AA1 7 CYS A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 HIS A 31 -1 O PHE A 25 N ILE A 18 SHEET 3 AA1 7 CYS A 34 PRO A 38 -1 O CYS A 34 N HIS A 31 SHEET 4 AA1 7 ASP A 69 LEU A 77 -1 O LEU A 75 N ALA A 35 SHEET 5 AA1 7 ARG A 52 THR A 63 -1 N LYS A 58 O TRP A 76 SHEET 6 AA1 7 SER A 46 ILE A 49 -1 N VAL A 47 O VAL A 54 SHEET 7 AA1 7 CYS A 15 THR A 20 -1 N THR A 19 O THR A 48 SHEET 1 AA2 7 TRP A 97 THR A 104 0 SHEET 2 AA2 7 LEU A 112 LEU A 127 -1 O VAL A 119 N TRP A 97 SHEET 3 AA2 7 ASN A 130 TYR A 138 -1 O LEU A 135 N TYR A 122 SHEET 4 AA2 7 GLY A 169 ALA A 173 -1 O GLY A 171 N LEU A 136 SHEET 5 AA2 7 ASN A 156 GLY A 164 -1 N GLY A 163 O TYR A 170 SHEET 6 AA2 7 VAL A 150 ASN A 153 -1 N ILE A 151 O ALA A 159 SHEET 7 AA2 7 TRP A 97 THR A 104 -1 N ALA A 103 O VAL A 150 SITE 1 AC1 22 ARG A 8 LYS A 22 HIS A 40 GLU A 71 SITE 2 AC1 22 PRO A 110 MET A 111 LEU A 127 SER A 128 SITE 3 AC1 22 ASN A 130 THR A 132 THR A 142 LYS A 143 SITE 4 AC1 22 PRO A 144 GLY A 145 CYS A 147 HIS A 161 SITE 5 AC1 22 VAL A 162 GLY A 163 GLY A 164 HOH A 606 SITE 6 AC1 22 HOH A 663 HOH A 691 CRYST1 52.903 95.626 98.853 90.00 90.00 90.00 C 2 2 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 0.018903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010457 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010116 0.00000