HEADER VIRAL PROTEIN 27-FEB-24 8S6F TITLE A STRUCTURAL INVESTIGATION OF THE INTERACTION BETWEEN A GC-376-BASED TITLE 2 PEPTIDOMIMETIC PROTAC AND ITS PRECURSOR WITH THE VIRAL MAIN PROTEASE TITLE 3 OF COXSACKIEVIRUS B3 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: COXSACKIEVIRUS B3; SOURCE 3 ORGANISM_TAXID: 12072; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 3C PROTEINASE, COXSACKIEVIRUS B3, PROTAC, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.DE SANTIS,D.GRIFAGNI,A.ORSETTI,E.LENCI,A.ROSATO,M.D'ONOFRIO, AUTHOR 2 A.TRABOCCHI,S.CIOFI-BAFFONI,F.CANTINI,V.CALDERONE REVDAT 1 04-DEC-24 8S6F 0 JRNL AUTH A.DE SANTIS,D.GRIFAGNI,A.ORSETTI,E.LENCI,A.ROSATO, JRNL AUTH 2 M.D'ONOFRIO,A.TRABOCCHI,S.CIOFI-BAFFONI,F.CANTINI, JRNL AUTH 3 V.CALDERONE JRNL TITL A STRUCTURAL INVESTIGATION OF THE INTERACTION BETWEEN A JRNL TITL 2 GC-376-BASED PEPTIDOMIMETIC PROTAC AND ITS PRECURSOR WITH JRNL TITL 3 THE VIRAL MAIN PROTEASE OF COXSACKIEVIRUS B3. JRNL REF BIOMOLECULES V. 14 2024 JRNL REFN ESSN 2218-273X JRNL PMID 39456193 JRNL DOI 10.3390/BIOM14101260 REMARK 2 REMARK 2 RESOLUTION. 1.93 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 12205 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 611 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 35.1300 - 3.0700 0.97 3025 160 0.1985 0.2056 REMARK 3 2 3.0700 - 2.4300 0.98 3010 158 0.2736 0.3251 REMARK 3 3 2.4300 - 2.1300 0.97 2970 157 0.2851 0.3613 REMARK 3 4 2.1300 - 1.9300 0.86 2589 136 0.3185 0.3217 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.780 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 : 0.003 1461 REMARK 3 ANGLE : 0.685 1969 REMARK 3 CHIRALITY : 0.047 215 REMARK 3 PLANARITY : 0.007 255 REMARK 3 DIHEDRAL : 7.980 220 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:180) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3366 0.2594 0.8054 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.1567 REMARK 3 T33: 0.2454 T12: -0.0204 REMARK 3 T13: 0.0597 T23: 0.0173 REMARK 3 L TENSOR REMARK 3 L11: 2.9630 L22: 5.3301 REMARK 3 L33: 3.0479 L12: -1.3006 REMARK 3 L13: -1.0565 L23: 1.7213 REMARK 3 S TENSOR REMARK 3 S11: -0.1321 S12: -0.0057 S13: -0.2638 REMARK 3 S21: 0.4752 S22: -0.0386 S23: 0.8657 REMARK 3 S31: 0.2338 S32: -0.0116 S33: 0.1278 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 8S6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292134166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-22 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 : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12210 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 47.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.90000 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 0.2 M MGCL2, 26% REMARK 280 PEG4000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 38.46000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.46000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.17500 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 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 -116.68 57.71 REMARK 500 ASN A 111 58.01 32.84 REMARK 500 ASN A 165 -124.67 -81.65 REMARK 500 PHE A 179 56.85 -117.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8OKC RELATED DB: PDB REMARK 900 SARS-COV2 NSP5 IN COMPLEX WITH A GC-376 BASED PEPTIDOMIMETIC PROTAC REMARK 900 RELATED ID: 8OKB RELATED DB: PDB REMARK 900 SARS-COV2 NSP5 IN COMPLEX WITH A PEPTIDOMIMETIC LIGAND DBREF 8S6F A 1 180 UNP P03313 POLG_CXB3N 1541 1720 SEQRES 1 A 180 GLY PRO ALA PHE GLU PHE ALA VAL ALA MET MET LYS ARG SEQRES 2 A 180 ASN SER SER THR VAL LYS THR GLU TYR GLY GLU PHE THR SEQRES 3 A 180 MET LEU GLY ILE TYR ASP ARG TRP ALA VAL LEU PRO ARG SEQRES 4 A 180 HIS ALA LYS PRO GLY PRO THR ILE LEU MET ASN ASP GLN SEQRES 5 A 180 GLU VAL GLY VAL LEU ASP ALA LYS GLU LEU VAL ASP LYS SEQRES 6 A 180 ASP GLY THR ASN LEU GLU LEU THR LEU LEU LYS LEU ASN SEQRES 7 A 180 ARG ASN GLU LYS PHE ARG ASP ILE ARG GLY PHE LEU ALA SEQRES 8 A 180 LYS GLU GLU VAL GLU VAL ASN GLU ALA VAL LEU ALA ILE SEQRES 9 A 180 ASN THR SER LYS PHE PRO ASN MET TYR ILE PRO VAL GLY SEQRES 10 A 180 GLN VAL THR GLU TYR GLY PHE LEU ASN LEU GLY GLY THR SEQRES 11 A 180 PRO THR LYS ARG MET LEU MET TYR ASN PHE PRO THR ARG SEQRES 12 A 180 ALA GLY GLN CYS GLY GLY VAL LEU MET SER THR GLY LYS SEQRES 13 A 180 VAL LEU GLY ILE HIS VAL GLY GLY ASN GLY HIS GLN GLY SEQRES 14 A 180 PHE SER ALA ALA LEU LEU LYS HIS TYR PHE ASN HET VQR A 201 33 HETNAM VQR METHYL (4~{S})-4-[[(2~{S})-4-METHYL-2- HETNAM 2 VQR (PHENYLMETHOXYCARBONYLAMINO)PENTANOYL]AMINO]-5- HETNAM 3 VQR [(3~{S})-2-OXIDANYLIDENEPYRROLIDIN-3-YL]PENTANOATE FORMUL 2 VQR C24 H35 N3 O6 FORMUL 3 HOH *65(H2 O) HELIX 1 AA1 GLY A 1 ASN A 14 1 14 HELIX 2 AA2 HIS A 40 LYS A 42 5 3 HELIX 3 AA3 ILE A 86 LEU A 90 5 5 HELIX 4 AA4 LEU A 175 ASN A 180 5 6 SHEET 1 AA1 7 SER A 15 THR A 20 0 SHEET 2 AA1 7 GLY A 23 TYR A 31 -1 O PHE A 25 N VAL A 18 SHEET 3 AA1 7 TRP A 34 PRO A 38 -1 O TRP A 34 N TYR 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 GLN A 52 VAL A 63 -1 N LYS A 60 O LEU A 74 SHEET 6 AA1 7 THR A 46 MET A 49 -1 N ILE A 47 O VAL A 54 SHEET 7 AA1 7 SER A 15 THR A 20 -1 N LYS A 19 O LEU A 48 SHEET 1 AA2 7 VAL A 97 ILE A 104 0 SHEET 2 AA2 7 MET A 112 LEU A 127 -1 O MET A 112 N ILE A 104 SHEET 3 AA2 7 THR A 130 TYR A 138 -1 O THR A 132 N LEU A 125 SHEET 4 AA2 7 GLY A 169 ALA A 173 -1 O SER A 171 N LEU A 136 SHEET 5 AA2 7 LYS A 156 GLY A 163 -1 N ILE A 160 O ALA A 172 SHEET 6 AA2 7 VAL A 150 SER A 153 -1 N LEU A 151 O LEU A 158 SHEET 7 AA2 7 VAL A 97 ILE A 104 -1 N VAL A 101 O MET A 152 LINK SG CYS A 147 C4 VQR A 201 1555 1555 1.71 CRYST1 76.920 64.350 38.990 90.00 115.72 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 0.013001 0.000000 0.006262 0.00000 SCALE2 0.000000 0.015540 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028468 0.00000 CONECT 1161 1418 CONECT 1400 1427 CONECT 1401 1421 1424 1429 CONECT 1402 1403 1425 1430 CONECT 1403 1402 1404 1426 CONECT 1404 1403 1405 CONECT 1405 1404 1406 1407 CONECT 1406 1405 CONECT 1407 1405 CONECT 1408 1426 1431 1432 CONECT 1409 1410 1432 CONECT 1410 1409 1412 1416 CONECT 1411 1417 1427 1428 CONECT 1412 1410 1413 CONECT 1413 1412 1414 CONECT 1414 1413 1415 CONECT 1415 1414 1416 CONECT 1416 1410 1415 CONECT 1417 1411 1418 CONECT 1418 1161 1417 1419 CONECT 1419 1418 1420 1425 CONECT 1420 1419 1421 CONECT 1421 1401 1420 1422 CONECT 1422 1421 1423 CONECT 1423 1422 1424 CONECT 1424 1401 1423 CONECT 1425 1402 1419 CONECT 1426 1403 1408 CONECT 1427 1400 1411 CONECT 1428 1411 CONECT 1429 1401 CONECT 1430 1402 CONECT 1431 1408 CONECT 1432 1408 1409 MASTER 232 0 1 4 14 0 0 6 1496 1 34 14 END