HEADER HYDROLASE 18-DEC-19 6LKA
TITLE CRYSTAL STRUCTURE OF EV71-3C PROTEASE WITH A NOVEL MACROCYCLIC
TITLE 2 COMPOUNDS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3C PROTEINASE;
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: ENTEROVIRUS A71;
SOURCE 3 ORGANISM_TAXID: 39054;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ENTEROVIRUS 71, 3C PROTEASE INHIBITOR, HYDROLASE INHIBITOR, VIRUS,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.LI,S.Q.WU,T.Y.C.XIAO,Y.L.LI,Z.M.SU,F.HAO,G.P.HU,J.HU,F.S.LIN,
AUTHOR 2 X.S.CHEN,Z.X.GU,H.Y.HE,J.LI,S.H.CHEN
REVDAT 3 20-NOV-24 6LKA 1 REMARK
REVDAT 2 22-NOV-23 6LKA 1 REMARK
REVDAT 1 17-JUN-20 6LKA 0
JRNL AUTH P.LI,S.WU,T.XIAO,Y.LI,Z.SU,W.WEI,F.HAO,G.HU,F.LIN,X.CHEN,
JRNL AUTH 2 Z.GU,T.LIN,H.HE,J.LI,S.CHEN
JRNL TITL DESIGN, SYNTHESIS, AND EVALUATION OF A NOVEL MACROCYCLIC
JRNL TITL 2 ANTI-EV71 AGENT.
JRNL REF BIOORG.MED.CHEM. V. 28 15551 2020
JRNL REFN ESSN 1464-3391
JRNL PMID 32503695
JRNL DOI 10.1016/J.BMC.2020.115551
REMARK 2
REMARK 2 RESOLUTION. 2.03 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.12_2829
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) : 2.03
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.32
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1
REMARK 3 NUMBER OF REFLECTIONS : 9968
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.202
REMARK 3 R VALUE (WORKING SET) : 0.196
REMARK 3 FREE R VALUE : 0.259
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920
REMARK 3 FREE R VALUE TEST SET COUNT : 989
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 32.3210 - 3.8875 0.86 1229 135 0.1492 0.1680
REMARK 3 2 3.8875 - 3.0864 0.94 1273 145 0.1587 0.2476
REMARK 3 3 3.0864 - 2.6965 0.97 1292 138 0.2289 0.3137
REMARK 3 4 2.6965 - 2.4501 0.99 1346 144 0.2551 0.3736
REMARK 3 5 2.4501 - 2.2745 1.00 1307 148 0.2500 0.3364
REMARK 3 6 2.2745 - 2.1404 1.00 1340 146 0.2692 0.3489
REMARK 3 7 2.1404 - 2.0333 0.91 1192 133 0.2780 0.3297
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) : 0.330
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.840
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.22
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 : 0.008 1483
REMARK 3 ANGLE : 1.017 2007
REMARK 3 CHIRALITY : 0.059 229
REMARK 3 PLANARITY : 0.005 259
REMARK 3 DIHEDRAL : 6.730 1228
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 12.9537 16.0999 -9.3203
REMARK 3 T TENSOR
REMARK 3 T11: 0.2782 T22: 0.2062
REMARK 3 T33: 0.2113 T12: -0.0284
REMARK 3 T13: 0.0755 T23: -0.0126
REMARK 3 L TENSOR
REMARK 3 L11: 0.9225 L22: 0.8758
REMARK 3 L33: 0.3778 L12: 0.2172
REMARK 3 L13: 0.0146 L23: 0.0659
REMARK 3 S TENSOR
REMARK 3 S11: 0.1073 S12: -0.0181 S13: 0.0644
REMARK 3 S21: 0.4192 S22: -0.1106 S23: 0.1718
REMARK 3 S31: 0.0704 S32: 0.0651 S33: 0.0007
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 6LKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-19.
REMARK 100 THE DEPOSITION ID IS D_1300014943.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-MAR-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
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 MICROMAX-007 HF
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 : MAR SCANNER 345 MM PLATE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOMAR
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9989
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030
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 (%) : 95.1
REMARK 200 DATA REDUNDANCY : 3.960
REMARK 200 R MERGE (I) : 0.06900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.42600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 4GHT
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 37.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 8.5, EVAPORATION,
REMARK 280 TEMPERATURE 298K
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 37.92750
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 37.92750
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 32.13500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.32050
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 32.13500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.32050
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.92750
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 32.13500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.32050
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.92750
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 32.13500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 32.32050
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 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 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 -124.90 44.89
REMARK 500 GLU A 50 -64.76 62.84
REMARK 500 HIS A 51 11.25 -148.89
REMARK 500 TYR A 122 -51.06 -156.93
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 417 DISTANCE = 6.21 ANGSTROMS
REMARK 525 HOH A 418 DISTANCE = 7.02 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EGF A 201
DBREF 6LKA A 1 180 UNP A9XG43 A9XG43_9ENTO 1549 1728
SEQADV 6LKA MET A 0 UNP A9XG43 EXPRESSION TAG
SEQRES 1 A 181 MET GLY PRO SER LEU ASP PHE ALA LEU SER LEU LEU ARG
SEQRES 2 A 181 ARG ASN VAL ARG GLN VAL GLN THR ASP GLN GLY HIS PHE
SEQRES 3 A 181 THR MET LEU GLY VAL ARG ASP ARG LEU ALA VAL LEU PRO
SEQRES 4 A 181 ARG HIS SER GLN PRO GLY LYS THR ILE TRP ILE GLU HIS
SEQRES 5 A 181 LYS LEU VAL ASN ILE LEU ASP ALA VAL GLU LEU VAL ASP
SEQRES 6 A 181 GLU GLN GLY VAL ASN LEU GLU LEU THR LEU ILE THR LEU
SEQRES 7 A 181 ASP THR ASN GLU LYS PHE ARG ASP ILE THR LYS PHE ILE
SEQRES 8 A 181 PRO GLU ASN ILE SER THR ALA SER ASP ALA THR LEU VAL
SEQRES 9 A 181 ILE ASN THR GLU HIS MET PRO SER MET PHE VAL PRO VAL
SEQRES 10 A 181 GLY ASP VAL VAL GLN TYR GLY PHE LEU ASN LEU SER GLY
SEQRES 11 A 181 LYS PRO THR HIS ARG THR MET MET TYR ASN PHE PRO THR
SEQRES 12 A 181 LYS ALA GLY GLN CYS GLY GLY VAL VAL THR SER VAL GLY
SEQRES 13 A 181 LYS VAL ILE GLY ILE HIS ILE GLY GLY ASN GLY ARG GLN
SEQRES 14 A 181 GLY PHE CYS ALA GLY LEU LYS ARG SER TYR PHE ALA
HET EGF A 201 46
HETNAM EGF ~{N}-[(2~{S})-1-[[(2~{S},3~{S},6~{S},7~{Z},12~{E})-4,9-
HETNAM 2 EGF BIS(OXIDANYLIDENE)-6-[[(3~{S})-2-
HETNAM 3 EGF OXIDANYLIDENEPYRROLIDIN-3-YL]METHYL]-2-PHENYL-1,10-
HETNAM 4 EGF DIOXA-5-AZACYCLOPENTADECA-7,12-DIEN-3-YL]AMINO]-3-
HETNAM 5 EGF METHYL-1-OXIDANYLIDENE-BUTAN-2-YL]-5-METHYL-1,2-
HETNAM 6 EGF OXAZOLE-3-CARBOXAMIDE
FORMUL 2 EGF C33 H41 N5 O8
FORMUL 3 HOH *118(H2 O)
HELIX 1 AA1 GLY A 1 ASN A 14 1 14
HELIX 2 AA2 HIS A 40 GLN A 42 5 3
HELIX 3 AA3 ILE A 86 ILE A 90 5 5
HELIX 4 AA4 LYS A 175 ALA A 180 5 6
SHEET 1 AA1 7 VAL A 15 THR A 20 0
SHEET 2 AA1 7 GLY A 23 ARG A 31 -1 O MET A 27 N ARG A 16
SHEET 3 AA1 7 LEU A 34 PRO A 38 -1 O LEU A 34 N ARG A 31
SHEET 4 AA1 7 ASN A 69 LEU A 77 -1 O THR A 73 N LEU A 37
SHEET 5 AA1 7 LYS A 52 VAL A 63 -1 N LEU A 62 O LEU A 72
SHEET 6 AA1 7 THR A 46 ILE A 49 -1 N ILE A 47 O VAL A 54
SHEET 7 AA1 7 VAL A 15 THR A 20 -1 N GLN A 19 O TRP A 48
SHEET 1 AA2 7 MET A 112 VAL A 114 0
SHEET 2 AA2 7 THR A 101 ILE A 104 -1 N LEU A 102 O VAL A 114
SHEET 3 AA2 7 VAL A 150 THR A 152 -1 O THR A 152 N THR A 101
SHEET 4 AA2 7 VAL A 157 GLY A 164 -1 O GLY A 159 N VAL A 151
SHEET 5 AA2 7 GLY A 169 GLY A 173 -1 O PHE A 170 N GLY A 163
SHEET 6 AA2 7 LYS A 130 TYR A 138 -1 N ARG A 134 O GLY A 173
SHEET 7 AA2 7 VAL A 120 LEU A 127 -1 N LEU A 127 O LYS A 130
LINK SG CYS A 147 C16 EGF A 201 1555 1555 1.77
SITE 1 AC1 17 ARG A 39 HIS A 40 GLU A 71 LEU A 125
SITE 2 AC1 17 ASN A 126 LEU A 127 SER A 128 THR A 142
SITE 3 AC1 17 LYS A 143 ALA A 144 GLY A 145 CYS A 147
SITE 4 AC1 17 HIS A 161 ILE A 162 GLY A 163 GLY A 164
SITE 5 AC1 17 HOH A 322
CRYST1 64.270 64.641 75.855 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 0.015559 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015470 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013183 0.00000