HEADER HYDROLASE 23-JUN-25 9VKK TITLE CRYSTAL STRUCTURE OF EV71 3C PROTEASE IN COMPLEX WITH BOFUTRELVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE 3C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PICORNAIN 3C,P3C; COMPND 5 EC: 3.4.22.28; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN ENTEROVIRUS 71 (STRAIN BRCR); SOURCE 3 ORGANISM_TAXID: 69153; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENTEROVIRUS, 3C PROTEASE, COMPLEX, BOFUTRELVIR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHANG,Z.YE REVDAT 1 01-APR-26 9VKK 0 JRNL AUTH Z.YE,W.DAI,S.ZHANG,Y.XIANG,J.WANG,Y.ZHANG,W.CAO,J.NEYTS, JRNL AUTH 2 Z.LI,F.FENG,G.XIAO,H.LIU,J.CAO,L.K.ZHANG JRNL TITL A CLINICAL SARS-COV-2 MPRO INHIBITOR BLOCKS REPLICATION OF JRNL TITL 2 MULTIPLE ENTEROVIRUSES AND CONFERS ORAL IN VIVO PROTECTION JRNL TITL 3 IN ANIMAL MODELS. JRNL REF PLOS PATHOG. V. 22 14051 2026 JRNL REFN ESSN 1553-7374 JRNL PMID 41811867 JRNL DOI 10.1371/JOURNAL.PPAT.1014051 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 7471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 357 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 28.9200 - 3.3200 0.94 2455 115 0.1616 0.1936 REMARK 3 2 3.3200 - 2.6300 0.84 2149 111 0.1651 0.2291 REMARK 3 3 2.6300 - 2.3000 1.00 2510 131 0.1837 0.2604 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.215 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.969 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.87 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 : 0.009 1469 REMARK 3 ANGLE : 1.276 1987 REMARK 3 CHIRALITY : 0.070 228 REMARK 3 PLANARITY : 0.008 260 REMARK 3 DIHEDRAL : 16.562 533 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 9VKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 30-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1300060827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-25 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.97861 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRIMETHYLAMINE N-OXIDE REMARK 280 DIHYDRATE, 0.1 M TRIS (PH 8.5), 20% POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 2,000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 39.10250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.30850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.10250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.30850 REMARK 290 SMTRY3 4 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: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 GLU A 182 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 362 O HOH A 396 2.09 REMARK 500 O HOH A 372 O HOH A 384 2.16 REMARK 500 O HOH A 309 O HOH A 364 2.16 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 ASN A 14 -20.43 -141.34 REMARK 500 ASP A 32 -108.55 46.03 REMARK 500 ASP A 99 61.85 37.05 REMARK 500 TYR A 122 -51.76 -122.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: ~{N}-[(2~{S})-3-CYCLOHEXYL-1-OXIDANYLIDENE-1-[[(2~{ REMARK 630 S})-1-OXIDANYLIDENE-3-[(3~{S})-2-OXIDANYLIDENEPYRROLIDIN-3-YL] REMARK 630 PROPAN-2-YL]AMINO]PROPAN-2-YL]-1~{H}-INDOLE-2-CARBOXAMIDE 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 FHR A 202 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ICB ALC ELL REMARK 630 DETAILS: NULL DBREF 9VKK A 2 182 UNP Q66478 POLG_HE71B 1550 1730 SEQADV 9VKK GLY A 0 UNP Q66478 EXPRESSION TAG SEQADV 9VKK SER A 1 UNP Q66478 EXPRESSION TAG SEQADV 9VKK PHE A 89 UNP Q66478 CYS 1637 CONFLICT SEQADV 9VKK MET A 109 UNP Q66478 ILE 1657 CONFLICT SEQADV 9VKK ALA A 144 UNP Q66478 PRO 1692 CONFLICT SEQADV 9VKK GLY A 169 UNP Q66478 ALA 1717 CONFLICT SEQRES 1 A 183 GLY SER PRO SER LEU ASP PHE ALA LEU SER LEU LEU ARG SEQRES 2 A 183 ARG ASN ILE ARG GLN ALA GLN THR ASP GLN GLY HIS PHE SEQRES 3 A 183 THR MET LEU GLY VAL ARG ASP ARG LEU ALA ILE LEU PRO SEQRES 4 A 183 ARG HIS SER GLN PRO GLY LYS THR ILE TRP VAL GLU HIS SEQRES 5 A 183 LYS LEU ILE ASN VAL LEU ASP ALA VAL GLU LEU VAL ASP SEQRES 6 A 183 GLU GLN GLY VAL ASN LEU GLU LEU THR LEU VAL THR LEU SEQRES 7 A 183 ASP THR ASN GLU LYS PHE ARG ASP ILE THR LYS PHE ILE SEQRES 8 A 183 PRO GLU VAL ILE THR GLY ALA SER ASP ALA THR LEU VAL SEQRES 9 A 183 ILE ASN THR GLU HIS MET PRO SER MET PHE VAL PRO VAL SEQRES 10 A 183 GLY ASP VAL VAL GLN TYR GLY PHE LEU ASN LEU SER GLY SEQRES 11 A 183 LYS PRO THR HIS ARG THR MET MET TYR ASN PHE PRO THR SEQRES 12 A 183 LYS ALA GLY GLN CYS GLY GLY VAL VAL THR SER VAL GLY SEQRES 13 A 183 LYS ILE ILE GLY ILE HIS ILE GLY GLY ASN GLY ARG GLN SEQRES 14 A 183 GLY PHE CYS ALA GLY LEU LYS ARG SER TYR PHE ALA SER SEQRES 15 A 183 GLU HET GOL A 201 6 HET FHR A 202 33 HETNAM GOL GLYCEROL HETNAM FHR ~{N}-[(2~{S})-3-CYCLOHEXYL-1-OXIDANYLIDENE-1-[[(2~{S})- HETNAM 2 FHR 1-OXIDANYLIDENE-3-[(3~{S})-2-OXIDANYLIDENEPYRROLIDIN- HETNAM 3 FHR 3-YL]PROPAN-2-YL]AMINO]PROPAN-2-YL]-1~{H}-INDOLE-2- HETNAM 4 FHR CARBOXAMIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 FHR C25 H32 N4 O4 FORMUL 4 HOH *101(H2 O) HELIX 1 AA1 LEU A 4 ASN A 14 1 11 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 ILE A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 ARG A 31 -1 O PHE A 25 N ALA A 18 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 ASP A 78 -1 O THR A 73 N LEU A 37 SHEET 5 AA1 7 LYS A 52 VAL A 63 -1 N ASN A 55 O ASP A 78 SHEET 6 AA1 7 THR A 46 VAL A 49 -1 N ILE A 47 O ILE A 54 SHEET 7 AA1 7 ILE A 15 THR A 20 -1 N GLN A 19 O TRP A 48 SHEET 1 AA2 7 ALA A 97 ILE A 104 0 SHEET 2 AA2 7 MET A 112 LEU A 125 -1 O VAL A 114 N LEU A 102 SHEET 3 AA2 7 THR A 132 TYR A 138 -1 O THR A 132 N LEU A 125 SHEET 4 AA2 7 GLY A 169 GLY A 173 -1 O GLY A 169 N TYR A 138 SHEET 5 AA2 7 LYS A 156 GLY A 164 -1 N ILE A 160 O ALA A 172 SHEET 6 AA2 7 VAL A 150 SER A 153 -1 N VAL A 151 O GLY A 159 SHEET 7 AA2 7 ALA A 97 ILE A 104 -1 N THR A 101 O THR A 152 LINK SG CYS A 147 C31 FHR A 202 1555 1555 1.77 CRYST1 78.205 46.617 51.920 90.00 106.64 90.00 C 1 2 1 4 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 0.012787 0.000000 0.003822 0.00000 SCALE2 0.000000 0.021451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020102 0.00000 CONECT 1162 1440 CONECT 1403 1404 1405 CONECT 1404 1403 CONECT 1405 1403 1406 1407 CONECT 1406 1405 CONECT 1407 1405 1408 CONECT 1408 1407 CONECT 1409 1417 1419 1420 CONECT 1410 1411 1415 CONECT 1411 1410 1412 CONECT 1412 1411 1413 CONECT 1413 1412 1414 1418 CONECT 1414 1413 1415 1416 CONECT 1415 1410 1414 CONECT 1416 1414 1417 CONECT 1417 1409 1416 1418 CONECT 1418 1413 1417 CONECT 1419 1409 CONECT 1420 1409 1421 CONECT 1421 1420 1422 1424 CONECT 1422 1421 1423 1439 CONECT 1423 1422 CONECT 1424 1421 1425 CONECT 1425 1424 1426 1430 CONECT 1426 1425 1427 CONECT 1427 1426 1428 CONECT 1428 1427 1429 CONECT 1429 1428 1430 CONECT 1430 1425 1429 CONECT 1431 1432 CONECT 1432 1431 1433 1436 CONECT 1433 1432 1434 CONECT 1434 1433 1435 CONECT 1435 1434 1436 CONECT 1436 1432 1435 1437 CONECT 1437 1436 1438 CONECT 1438 1437 1439 1440 CONECT 1439 1422 1438 CONECT 1440 1162 1438 1441 CONECT 1441 1440 MASTER 251 0 2 4 14 0 0 6 1541 1 40 15 END