HEADER VIRAL PROTEIN/INHIBITOR 19-FEB-23 8IFS TITLE SARS-COV-2 3CL PROTEASE (3CLPRO) IN COMPLEX WITH COMPOUND 7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: 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 MPRO, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.X.SU,W.F.ZHAO,H.XIE,T.Q.NIE,M.J.LI,Y.C.XU REVDAT 3 08-MAY-24 8IFS 1 JRNL REVDAT 2 01-MAY-24 8IFS 1 JRNL REVDAT 1 18-OCT-23 8IFS 0 JRNL AUTH X.JIANG,H.SU,W.SHANG,F.ZHOU,Y.ZHANG,W.ZHAO,Q.ZHANG,H.XIE, JRNL AUTH 2 L.JIANG,T.NIE,F.YANG,M.XIONG,X.HUANG,M.LI,P.CHEN,S.PENG, JRNL AUTH 3 G.XIAO,H.JIANG,R.TANG,L.ZHANG,J.SHEN,Y.XU JRNL TITL STRUCTURE-BASED DEVELOPMENT AND PRECLINICAL EVALUATION OF JRNL TITL 2 THE SARS-COV-2 3C-LIKE PROTEASE INHIBITOR SIMNOTRELVIR. JRNL REF NAT COMMUN V. 14 6463 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37833261 JRNL DOI 10.1038/S41467-023-42102-Y REMARK 2 REMARK 2 RESOLUTION. 2.46 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1 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) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 26356 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.268 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1288 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 27.0000 - 5.1000 0.96 2903 125 0.1998 0.2102 REMARK 3 2 5.1000 - 4.0500 0.99 2943 127 0.2042 0.2141 REMARK 3 3 4.0500 - 3.5400 0.72 2090 130 0.2762 0.3689 REMARK 3 4 3.5400 - 3.2200 0.97 2839 147 0.2983 0.2594 REMARK 3 5 3.2200 - 2.9900 0.98 2855 144 0.3076 0.3904 REMARK 3 6 2.9900 - 2.8100 0.98 2868 147 0.3246 0.3321 REMARK 3 7 2.8100 - 2.6700 0.98 2836 178 0.3450 0.3779 REMARK 3 8 2.6700 - 2.5600 0.98 2847 141 0.3755 0.3534 REMARK 3 9 2.5600 - 2.4600 0.99 2887 149 0.3942 0.4027 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 40.680 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 4632 REMARK 3 ANGLE : 0.662 6329 REMARK 3 CHIRALITY : 0.045 731 REMARK 3 PLANARITY : 0.005 818 REMARK 3 DIHEDRAL : 11.182 1619 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.0153 28.6639 9.9139 REMARK 3 T TENSOR REMARK 3 T11: 0.3683 T22: 0.2699 REMARK 3 T33: 0.4175 T12: -0.0218 REMARK 3 T13: 0.0420 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 0.0921 L22: 0.0471 REMARK 3 L33: 0.0489 L12: -0.0003 REMARK 3 L13: 0.0343 L23: 0.0606 REMARK 3 S TENSOR REMARK 3 S11: 0.0849 S12: 0.1917 S13: 0.1948 REMARK 3 S21: 0.0095 S22: -0.1254 S23: 0.0928 REMARK 3 S31: 0.1144 S32: -0.0225 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2877 17.8923 17.1988 REMARK 3 T TENSOR REMARK 3 T11: 0.3326 T22: 0.2962 REMARK 3 T33: 0.3013 T12: -0.0519 REMARK 3 T13: 0.0185 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.0886 L22: -0.0138 REMARK 3 L33: -0.0354 L12: 0.0549 REMARK 3 L13: -0.0466 L23: -0.0523 REMARK 3 S TENSOR REMARK 3 S11: 0.1053 S12: -0.2627 S13: 0.1791 REMARK 3 S21: 0.0530 S22: -0.1835 S23: -0.0341 REMARK 3 S31: 0.1474 S32: -0.1098 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.6748 -0.9607 35.2277 REMARK 3 T TENSOR REMARK 3 T11: 0.3480 T22: 0.8267 REMARK 3 T33: 0.0573 T12: -0.1040 REMARK 3 T13: -0.0195 T23: 0.6674 REMARK 3 L TENSOR REMARK 3 L11: 0.0189 L22: 0.0285 REMARK 3 L33: 0.0663 L12: 0.0033 REMARK 3 L13: 0.0124 L23: -0.0599 REMARK 3 S TENSOR REMARK 3 S11: 0.1896 S12: -0.7131 S13: -0.2744 REMARK 3 S21: -0.0596 S22: 0.2535 S23: 0.0344 REMARK 3 S31: -0.0377 S32: 0.1422 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.7034 26.1777 28.3976 REMARK 3 T TENSOR REMARK 3 T11: 0.3472 T22: 0.5222 REMARK 3 T33: 0.3342 T12: -0.1288 REMARK 3 T13: -0.0237 T23: -0.4400 REMARK 3 L TENSOR REMARK 3 L11: 0.0415 L22: 0.0075 REMARK 3 L33: 0.0230 L12: 0.0134 REMARK 3 L13: 0.0325 L23: -0.0125 REMARK 3 S TENSOR REMARK 3 S11: 0.0836 S12: -0.3422 S13: 0.0370 REMARK 3 S21: 0.0138 S22: -0.2637 S23: -0.2160 REMARK 3 S31: 0.0602 S32: -0.0063 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 85 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.1991 30.1320 39.3008 REMARK 3 T TENSOR REMARK 3 T11: 0.4166 T22: 0.6141 REMARK 3 T33: 0.3496 T12: -0.0841 REMARK 3 T13: 0.0459 T23: -0.8508 REMARK 3 L TENSOR REMARK 3 L11: -0.0049 L22: 0.0010 REMARK 3 L33: 0.0039 L12: -0.0024 REMARK 3 L13: -0.0013 L23: 0.0164 REMARK 3 S TENSOR REMARK 3 S11: 0.0799 S12: -0.2619 S13: -0.0525 REMARK 3 S21: 0.0997 S22: 0.0564 S23: 0.1275 REMARK 3 S31: 0.0263 S32: -0.1279 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 86 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.6703 21.5721 25.0071 REMARK 3 T TENSOR REMARK 3 T11: 0.3189 T22: 0.3809 REMARK 3 T33: 0.3661 T12: -0.0767 REMARK 3 T13: 0.0135 T23: -0.1863 REMARK 3 L TENSOR REMARK 3 L11: 0.0453 L22: 0.0232 REMARK 3 L33: -0.0595 L12: 0.0168 REMARK 3 L13: -0.0680 L23: -0.0157 REMARK 3 S TENSOR REMARK 3 S11: 0.1402 S12: -0.2065 S13: 0.2976 REMARK 3 S21: -0.0601 S22: -0.1154 S23: -0.0719 REMARK 3 S31: 0.1866 S32: 0.0767 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 167 THROUGH 226 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.7695 5.4224 18.6027 REMARK 3 T TENSOR REMARK 3 T11: 0.3114 T22: 0.2492 REMARK 3 T33: 0.3102 T12: -0.1021 REMARK 3 T13: -0.0647 T23: -0.2909 REMARK 3 L TENSOR REMARK 3 L11: 0.0432 L22: 0.0032 REMARK 3 L33: -0.0403 L12: 0.0093 REMARK 3 L13: 0.0363 L23: 0.1339 REMARK 3 S TENSOR REMARK 3 S11: 0.0489 S12: -0.0280 S13: -0.1338 REMARK 3 S21: 0.2188 S22: -0.0377 S23: 0.0787 REMARK 3 S31: -0.0527 S32: -0.1292 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 227 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.3934 -5.1344 10.8581 REMARK 3 T TENSOR REMARK 3 T11: 0.4042 T22: 0.6029 REMARK 3 T33: 0.6180 T12: -0.1339 REMARK 3 T13: 0.0730 T23: -0.2940 REMARK 3 L TENSOR REMARK 3 L11: 0.0069 L22: 0.0003 REMARK 3 L33: -0.0025 L12: -0.0057 REMARK 3 L13: 0.0042 L23: -0.0022 REMARK 3 S TENSOR REMARK 3 S11: -0.0672 S12: 0.0210 S13: 0.0020 REMARK 3 S21: 0.0293 S22: -0.0318 S23: 0.1057 REMARK 3 S31: -0.0308 S32: -0.0664 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 244 THROUGH 300 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.3159 1.1585 7.6117 REMARK 3 T TENSOR REMARK 3 T11: 0.3369 T22: 0.2510 REMARK 3 T33: 0.3749 T12: -0.0556 REMARK 3 T13: -0.0594 T23: -0.1194 REMARK 3 L TENSOR REMARK 3 L11: 0.0088 L22: 0.0636 REMARK 3 L33: 0.0366 L12: 0.0045 REMARK 3 L13: -0.0112 L23: 0.0123 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: 0.2635 S13: -0.2583 REMARK 3 S21: 0.1507 S22: -0.1872 S23: 0.0688 REMARK 3 S31: -0.1130 S32: -0.1019 S33: -0.0000 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 8IFS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-22 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27141 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.460 REMARK 200 RESOLUTION RANGE LOW (A) : 59.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.46 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.63400 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, PH5.5-6.5, 10%-25% REMARK 280 PEG6000, 3% DMSO, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 41.05300 REMARK 290 SMTRY3 2 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: 2520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 301 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 SER B 301 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 REMARK 465 GLN B 306 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 GLU A 47 CG CD OE1 OE2 REMARK 470 ASN A 51 CG OD1 ND2 REMARK 470 LEU A 67 CG CD1 CD2 REMARK 470 ASN A 72 CG OD1 ND2 REMARK 470 VAL A 73 CG1 CG2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 GLN A 110 CG CD OE1 NE2 REMARK 470 ASP A 153 CG OD1 OD2 REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 ASP A 216 CG OD1 OD2 REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 THR A 226 OG1 CG2 REMARK 470 ASN A 228 CG OD1 ND2 REMARK 470 LEU A 232 CG CD1 CD2 REMARK 470 MET A 235 CG SD CE REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 GLN A 256 CG CD OE1 NE2 REMARK 470 LEU A 262 CG CD1 CD2 REMARK 470 ASN A 277 CG OD1 ND2 REMARK 470 ARG A 279 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 294 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 298 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 47 CG CD OE1 OE2 REMARK 470 LEU B 67 CG CD1 CD2 REMARK 470 ASN B 72 CG OD1 ND2 REMARK 470 GLN B 74 CG CD OE1 NE2 REMARK 470 ARG B 76 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 92 CG OD1 OD2 REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 GLN B 110 CG CD OE1 NE2 REMARK 470 ASP B 153 CG OD1 OD2 REMARK 470 TYR B 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP B 155 CG OD1 OD2 REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 THR B 226 OG1 CG2 REMARK 470 ASN B 228 CG OD1 ND2 REMARK 470 LEU B 232 CG CD1 CD2 REMARK 470 VAL B 233 CG1 CG2 REMARK 470 MET B 235 CG SD CE REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LEU B 262 CG CD1 CD2 REMARK 470 ASN B 277 CG OD1 ND2 REMARK 470 ARG B 279 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 286 CG CD1 CD2 REMARK 470 PHE B 294 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 298 CG CD NE CZ NH1 NH2 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 SG CYS A 145 C8 OZL A 401 1.82 REMARK 500 SG CYS B 145 C8 OZL B 401 1.83 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 -124.42 53.87 REMARK 500 ASN A 84 -116.32 53.79 REMARK 500 TYR A 154 -71.56 -133.65 REMARK 500 ASP B 33 -125.26 51.94 REMARK 500 ASN B 84 -115.59 53.95 REMARK 500 TYR B 154 -65.38 -125.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IFS A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 8IFS B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 SEQRES 1 A 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 306 CYS SER GLY VAL THR PHE GLN SEQRES 1 B 306 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 B 306 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 B 306 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 B 306 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 B 306 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 B 306 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 B 306 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 B 306 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 B 306 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 B 306 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 B 306 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 B 306 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 B 306 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 B 306 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 B 306 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 B 306 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 B 306 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 B 306 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 B 306 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 B 306 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 B 306 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 B 306 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 B 306 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 B 306 CYS SER GLY VAL THR PHE GLN HET OZL A 401 37 HET OZL B 401 37 HETNAM OZL (8~{S})-7-[(2~{S})-2-(~{TERT}-BUTYLCARBAMOYLAMINO)-3,3- HETNAM 2 OZL DIMETHYL-BUTANOYL]-~{N}-[(1~{S})-1-CYANO-2-[(3~{S})-2- HETNAM 3 OZL OXIDANYLIDENEPYRROLIDIN-3-YL]ETHYL]-1,4-DITHIA-7- HETNAM 4 OZL AZASPIRO[4.4]NONANE-8-CARBOXAMIDE FORMUL 3 OZL 2(C25 H40 N6 O4 S2) FORMUL 5 HOH *9(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 ASN A 53 ARG A 60 1 8 HELIX 4 AA4 SER A 62 HIS A 64 5 3 HELIX 5 AA5 ILE A 200 ASN A 214 1 15 HELIX 6 AA6 THR A 226 MET A 235 1 10 HELIX 7 AA7 LYS A 236 ASN A 238 5 3 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 HELIX 12 AB3 SER B 10 GLY B 15 1 6 HELIX 13 AB4 HIS B 41 CYS B 44 5 4 HELIX 14 AB5 ASN B 53 ARG B 60 1 8 HELIX 15 AB6 SER B 62 HIS B 64 5 3 HELIX 16 AB7 ILE B 200 ASN B 214 1 15 HELIX 17 AB8 THR B 226 TYR B 237 1 12 HELIX 18 AB9 THR B 243 LEU B 250 1 8 HELIX 19 AC1 LEU B 250 GLY B 258 1 9 HELIX 20 AC2 ALA B 260 GLY B 275 1 16 HELIX 21 AC3 THR B 292 CYS B 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 VAL A 68 O LEU A 75 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 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 O LYS A 90 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ILE A 152 -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 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N SER B 81 O LYS B 88 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 VAL B 157 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ILE B 152 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O SER B 123 N ALA B 116 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 VAL B 157 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 CRYST1 54.542 82.106 86.394 90.00 96.91 90.00 P 1 21 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 0.018334 0.000000 0.002221 0.00000 SCALE2 0.000000 0.012179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011660 0.00000