HEADER VIRAL PROTEIN,HYDROLASE/INHIBITOR 22-FEB-24 8W3T TITLE CRYSTAL STRUCTURE OF ENTEROVIRUS 68 3C PROTEASE WITH GC376 AT 1.98 TITLE 2 ANGSTROMS 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: ENTEROVIRUS D68; SOURCE 3 ORGANISM_TAXID: 42789; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PROTEASE, HYDROLASE, ENTEROVIRUS, 3C PROTEIN, EV68, INHIBITOR, VIRAL KEYWDS 2 PROTEIN, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR V.N.AZZOLINO,A.M.SHAQRA,C.A.SCHIFFER REVDAT 1 15-JAN-25 8W3T 0 JRNL AUTH V.N.AZZOLINO,A.M.SHAQRA,A.ALI,N.K.YILMAZ,C.A.SCHIFFER JRNL TITL STRUCTURAL ANALYSIS OF INHIBITOR BINDING TO ENTEROVIRUS-D68 JRNL TITL 2 3C PROTEASE JRNL REF VIRUSES 2025 JRNL REFN ESSN 1999-4915 JRNL DOI 10.3390/V17010075 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122+SVN 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 22471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1109 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 32.0700 - 3.9600 1.00 2872 150 0.1576 0.1689 REMARK 3 2 3.9600 - 3.1400 1.00 2706 138 0.1879 0.2642 REMARK 3 3 3.1400 - 2.7500 1.00 2694 145 0.2114 0.2393 REMARK 3 4 2.7500 - 2.4900 1.00 2643 142 0.2497 0.2910 REMARK 3 5 2.4900 - 2.3200 0.99 2616 130 0.2244 0.2250 REMARK 3 6 2.3200 - 2.1800 0.99 2619 133 0.2659 0.3286 REMARK 3 7 2.1800 - 2.0500 0.99 2581 136 0.2790 0.3434 REMARK 3 8 2.0500 - 1.9800 0.99 2631 135 0.3338 0.4287 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) : 0.254 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.815 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.95 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 : 0.010 1527 REMARK 3 ANGLE : 1.139 2077 REMARK 3 CHIRALITY : 0.066 235 REMARK 3 PLANARITY : 0.010 270 REMARK 3 DIHEDRAL : 7.721 213 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 8W3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281808. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22473 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 32.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.07 M SODIUM ACETATE PEG4000 6-15% REMARK 280 GLYCEROL 10-35%, PH 4.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.87633 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.75267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.75267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 56.87633 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 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 189 REMARK 465 HIS A 190 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 LYS A 12 CG CD CE NZ REMARK 470 LYS A 108 CE NZ REMARK 470 ASP A 181 CG OD1 OD2 REMARK 470 LYS A 184 CG CD CE NZ 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 -116.76 46.97 REMARK 500 THR A 182 -105.73 -126.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR A 152 THR A 153 149.18 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 442 DISTANCE = 6.50 ANGSTROMS DBREF 8W3T A 1 182 UNP A1E4A3 A1E4A3_HED68 1549 1730 SEQADV 8W3T ALA A 183 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T LYS A 184 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 185 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 186 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 187 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 188 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 189 UNP A1E4A3 EXPRESSION TAG SEQADV 8W3T HIS A 190 UNP A1E4A3 EXPRESSION TAG SEQRES 1 A 190 GLY PRO GLY PHE ASP PHE ALA GLN ALA ILE MET LYS LYS SEQRES 2 A 190 ASN THR VAL VAL ALA ARG THR GLU LYS GLY GLU PHE THR SEQRES 3 A 190 MET LEU GLY VAL HIS ASP ARG VAL ALA VAL ILE PRO THR SEQRES 4 A 190 HIS ALA SER VAL GLY GLU THR ILE TYR ILE ASN ASP VAL SEQRES 5 A 190 GLU THR LYS VAL LEU ASP ALA CYS ALA LEU ARG ASP LEU SEQRES 6 A 190 THR ASP THR ASN LEU GLU ILE THR ILE VAL LYS LEU ASP SEQRES 7 A 190 ARG ASN GLN LYS PHE ARG ASP ILE ARG HIS PHE LEU PRO SEQRES 8 A 190 ARG TYR GLU ASP ASP TYR ASN ASP ALA VAL LEU SER VAL SEQRES 9 A 190 HIS THR SER LYS PHE PRO ASN MET TYR ILE PRO VAL GLY SEQRES 10 A 190 GLN VAL THR ASN TYR GLY PHE LEU ASN LEU GLY GLY THR SEQRES 11 A 190 PRO THR HIS ARG ILE LEU MET TYR ASN PHE PRO THR ARG SEQRES 12 A 190 ALA GLY GLN CYS GLY GLY VAL VAL THR THR THR GLY LYS SEQRES 13 A 190 VAL ILE GLY ILE HIS VAL GLY GLY ASN GLY ALA GLN GLY SEQRES 14 A 190 PHE ALA ALA MET LEU LEU HIS SER TYR PHE THR ASP THR SEQRES 15 A 190 ALA LYS HIS HIS HIS HIS HIS HIS HET UED A 201 59 HETNAM UED N~2~-[(BENZYLOXY)CARBONYL]-N-{(2S)-1-HYDROXY-3-[(3S)-2- HETNAM 2 UED OXOPYRROLIDIN-3-YL]PROPAN-2-YL}-L-LEUCINAMIDE HETSYN UED GC373 BOUND FORM, GC376 BOUND FORM FORMUL 2 UED C21 H31 N3 O5 FORMUL 3 HOH *142(H2 O) HELIX 1 AA1 GLY A 3 ASN A 14 1 12 HELIX 2 AA2 HIS A 40 SER A 42 5 3 HELIX 3 AA3 ILE A 86 LEU A 90 5 5 HELIX 4 AA4 LEU A 175 THR A 180 5 6 SHEET 1 AA1 7 THR A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 HIS A 31 -1 O PHE A 25 N ALA A 18 SHEET 3 AA1 7 VAL A 34 PRO A 38 -1 O VAL A 34 N HIS A 31 SHEET 4 AA1 7 ASN A 69 LEU A 77 -1 O VAL A 75 N ALA A 35 SHEET 5 AA1 7 VAL A 52 ARG A 63 -1 N LEU A 62 O ILE A 72 SHEET 6 AA1 7 THR A 46 ILE A 49 -1 N ILE A 47 O THR A 54 SHEET 7 AA1 7 THR A 15 THR A 20 -1 N ARG A 19 O TYR A 48 SHEET 1 AA2 7 TYR A 97 VAL A 104 0 SHEET 2 AA2 7 MET A 112 LEU A 127 -1 O ILE A 114 N LEU A 102 SHEET 3 AA2 7 THR A 130 TYR A 138 -1 O MET A 137 N THR A 120 SHEET 4 AA2 7 GLY A 169 MET A 173 -1 O ALA A 171 N LEU A 136 SHEET 5 AA2 7 LYS A 156 GLY A 164 -1 N VAL A 162 O PHE A 170 SHEET 6 AA2 7 VAL A 150 THR A 153 -1 N VAL A 151 O GLY A 159 SHEET 7 AA2 7 TYR A 97 VAL A 104 -1 N VAL A 101 O THR A 152 LINK SG CYS A 147 C21 UED A 201 1555 1555 1.77 CRYST1 56.174 56.174 170.629 90.00 90.00 120.00 P 31 2 1 6 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 0.017802 0.010278 0.000000 0.00000 SCALE2 0.000000 0.020556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005861 0.00000