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 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 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 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