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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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