HEADER VIRAL PROTEIN/INHIBITOR 05-MAR-24 8YKN TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE K90R MUTANT IN COMPLEX TITLE 2 WITH X77 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 11; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NSP11; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,J.ZHANG,J.LI REVDAT 1 27-NOV-24 8YKN 0 JRNL AUTH H.JIANG,W.LI,X.ZHOU,J.ZHANG,J.LI JRNL TITL CRYSTAL STRUCTURES OF CORONAVIRAL MAIN PROTEASES IN COMPLEX JRNL TITL 2 WITH THE NON-COVALENT INHIBITOR X77. JRNL REF INT.J.BIOL.MACROMOL. V. 276 33706 2024 JRNL REFN ISSN 0141-8130 JRNL PMID 38981557 JRNL DOI 10.1016/J.IJBIOMAC.2024.133706 REMARK 2 REMARK 2 RESOLUTION. 1.77 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 26636 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.986 REMARK 3 FREE R VALUE TEST SET COUNT : 1328 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 34.4300 - 3.6761 1.00 2902 163 0.1750 0.1829 REMARK 3 2 3.6761 - 2.9183 1.00 2885 136 0.1981 0.2263 REMARK 3 3 2.9183 - 2.5496 1.00 2796 168 0.2215 0.2658 REMARK 3 4 2.5496 - 2.3165 1.00 2835 170 0.2244 0.2612 REMARK 3 5 2.3165 - 2.1505 1.00 2822 143 0.2214 0.2743 REMARK 3 6 2.1505 - 2.0237 1.00 2847 129 0.2233 0.2594 REMARK 3 7 2.0237 - 1.9224 1.00 2825 141 0.2238 0.2778 REMARK 3 8 1.9224 - 1.8387 1.00 2811 151 0.2459 0.3027 REMARK 3 9 1.8387 - 1.7700 0.91 2585 127 0.2656 0.3021 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.508 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.72 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.71 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 : 0.007 2432 REMARK 3 ANGLE : 1.000 3308 REMARK 3 CHIRALITY : 0.061 370 REMARK 3 PLANARITY : 0.006 429 REMARK 3 DIHEDRAL : 12.440 1417 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 8YKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300043865. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-23 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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 34.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.92700 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 (%): 40.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12~0.21M PEG3350,20%~24%NA2SO4, REMARK 280 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 57.08600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.19350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.08600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.19350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 590 LIES ON A SPECIAL POSITION. 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 NH2 ARG A 298 O HOH A 501 2.09 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 ASP A 33 -131.14 52.94 REMARK 500 ASN A 51 73.43 -150.05 REMARK 500 ASN A 84 -119.61 51.11 REMARK 500 TYR A 154 -93.97 49.85 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YKN A 2 304 UNP P0DTC1 R1A_SARS2 3265 3567 SEQADV 8YKN ARG A 90 UNP P0DTC1 LYS 3353 ENGINEERED MUTATION SEQRES 1 A 303 GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL GLU SEQRES 2 A 303 GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR LEU SEQRES 3 A 303 ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO ARG SEQRES 4 A 303 HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO ASN SEQRES 5 A 303 TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN PHE SEQRES 6 A 303 LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE GLY SEQRES 7 A 303 HIS SER MET GLN ASN CYS VAL LEU LYS LEU ARG VAL ASP SEQRES 8 A 303 THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL ARG SEQRES 9 A 303 ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS TYR SEQRES 10 A 303 ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET ARG SEQRES 11 A 303 PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SER SEQRES 12 A 303 CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS VAL SEQRES 13 A 303 SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR GLY SEQRES 14 A 303 VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR GLY SEQRES 15 A 303 PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY THR SEQRES 16 A 303 ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU TYR SEQRES 17 A 303 ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN ARG SEQRES 18 A 303 PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA MET SEQRES 19 A 303 LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL ASP SEQRES 20 A 303 ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA VAL SEQRES 21 A 303 LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN ASN SEQRES 22 A 303 GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU LEU SEQRES 23 A 303 GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN CYS SEQRES 24 A 303 SER GLY VAL THR HET X77 A 401 34 HETNAM X77 N-(4-TERT-BUTYLPHENYL)-N-[(1R)-2-(CYCLOHEXYLAMINO)-2- HETNAM 2 X77 OXO-1-(PYRIDIN-3-YL)ETHYL]-1H-IMIDAZOLE-4-CARBOXAMIDE FORMUL 2 X77 C27 H33 N5 O2 FORMUL 3 HOH *125(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 THR A 45 MET A 49 5 5 HELIX 4 AA4 ASN A 53 LYS A 61 1 9 HELIX 5 AA5 SER A 62 HIS A 64 5 3 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 TYR A 237 1 12 HELIX 8 AA8 THR A 243 LEU A 250 1 8 HELIX 9 AA9 LEU A 250 GLY A 258 1 9 HELIX 10 AB1 ALA A 260 GLY A 275 1 16 HELIX 11 AB2 THR A 292 CYS A 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 PHE A 66 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 89 N VAL A 36 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 O ARG A 90 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 CRYST1 114.172 54.387 45.470 90.00 100.87 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 0.008759 0.000000 0.001682 0.00000 SCALE2 0.000000 0.018387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022394 0.00000