HEADER VIRAL PROTEIN/INHIBITOR 19-FEB-23 8IFR TITLE SARS-COV-2 3CL PROTEASE (3CLPRO) IN COMPLEX WITH COMPOUND 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A; 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 8IFR 1 JRNL REVDAT 2 01-MAY-24 8IFR 1 JRNL REVDAT 1 18-OCT-23 8IFR 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. 1.66 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) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 36567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1851 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 30.7900 - 3.9100 1.00 2891 151 0.1493 0.1706 REMARK 3 2 3.9100 - 3.1000 1.00 2746 153 0.1644 0.1993 REMARK 3 3 3.1000 - 2.7100 1.00 2717 136 0.1837 0.2224 REMARK 3 4 2.7100 - 2.4600 1.00 2708 132 0.1881 0.2276 REMARK 3 5 2.4600 - 2.2900 1.00 2658 152 0.1893 0.2437 REMARK 3 6 2.2900 - 2.1500 0.99 2679 127 0.1871 0.2398 REMARK 3 7 2.1500 - 2.0400 0.99 2655 136 0.1827 0.2077 REMARK 3 8 2.0400 - 1.9500 0.99 2628 143 0.1979 0.2180 REMARK 3 9 1.9500 - 1.8800 0.99 2610 144 0.2064 0.2431 REMARK 3 10 1.8800 - 1.8100 0.99 2650 141 0.2204 0.2700 REMARK 3 11 1.8100 - 1.7600 0.99 2608 140 0.2511 0.2783 REMARK 3 12 1.7600 - 1.7100 0.98 2587 151 0.2710 0.3110 REMARK 3 13 1.7100 - 1.6600 0.98 2579 145 0.2990 0.3173 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.390 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 : 0.006 2419 REMARK 3 ANGLE : 0.853 3299 REMARK 3 CHIRALITY : 0.052 378 REMARK 3 PLANARITY : 0.006 426 REMARK 3 DIHEDRAL : 14.315 865 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.9476 22.2250 -37.1629 REMARK 3 T TENSOR REMARK 3 T11: 0.1632 T22: 0.1471 REMARK 3 T33: 0.1506 T12: 0.0036 REMARK 3 T13: 0.0189 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 1.7921 L22: 1.2818 REMARK 3 L33: 2.3951 L12: 0.4540 REMARK 3 L13: 1.2415 L23: 0.2827 REMARK 3 S TENSOR REMARK 3 S11: -0.1112 S12: 0.1812 S13: -0.0198 REMARK 3 S21: -0.1425 S22: 0.0341 S23: 0.0711 REMARK 3 S31: 0.0014 S32: 0.0499 S33: 0.0734 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0065 11.3963 -39.3099 REMARK 3 T TENSOR REMARK 3 T11: 0.3156 T22: 0.3676 REMARK 3 T33: 0.3542 T12: -0.1061 REMARK 3 T13: -0.0327 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 0.9054 L22: 1.7560 REMARK 3 L33: 2.4994 L12: 0.8690 REMARK 3 L13: -0.6914 L23: -1.8181 REMARK 3 S TENSOR REMARK 3 S11: 0.0107 S12: 0.1408 S13: -0.0150 REMARK 3 S21: -0.1575 S22: 0.1614 S23: 0.4561 REMARK 3 S31: 0.3414 S32: -0.4679 S33: -0.2141 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2302 15.8934 -47.0210 REMARK 3 T TENSOR REMARK 3 T11: 0.2874 T22: 0.2540 REMARK 3 T33: 0.1985 T12: -0.0159 REMARK 3 T13: 0.0014 T23: -0.0662 REMARK 3 L TENSOR REMARK 3 L11: 2.0425 L22: 1.2797 REMARK 3 L33: 3.0251 L12: 0.8634 REMARK 3 L13: -0.2626 L23: -0.2667 REMARK 3 S TENSOR REMARK 3 S11: -0.1720 S12: 0.3392 S13: -0.1001 REMARK 3 S21: -0.2961 S22: 0.1742 S23: 0.0564 REMARK 3 S31: 0.2985 S32: -0.1411 S33: -0.0367 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 100 THROUGH 167 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.1905 20.1101 -29.3955 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.1520 REMARK 3 T33: 0.1555 T12: 0.0032 REMARK 3 T13: 0.0143 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 1.6470 L22: 1.6692 REMARK 3 L33: 3.1307 L12: 0.2468 REMARK 3 L13: 0.8412 L23: -0.3529 REMARK 3 S TENSOR REMARK 3 S11: -0.0202 S12: 0.1404 S13: -0.1296 REMARK 3 S21: -0.0154 S22: -0.0490 S23: -0.0751 REMARK 3 S31: 0.0492 S32: 0.3104 S33: 0.0707 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 168 THROUGH 185 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.6734 12.2819 -25.9342 REMARK 3 T TENSOR REMARK 3 T11: 0.1852 T22: 0.1723 REMARK 3 T33: 0.1765 T12: 0.0039 REMARK 3 T13: -0.0017 T23: 0.0250 REMARK 3 L TENSOR REMARK 3 L11: 3.7344 L22: 5.1126 REMARK 3 L33: 2.1485 L12: 0.9118 REMARK 3 L13: 1.4286 L23: -1.3369 REMARK 3 S TENSOR REMARK 3 S11: 0.0224 S12: -0.1024 S13: -0.4075 REMARK 3 S21: 0.1573 S22: -0.1202 S23: -0.1420 REMARK 3 S31: 0.3746 S32: 0.0033 S33: 0.0516 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 186 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.0782 17.4216 -16.0250 REMARK 3 T TENSOR REMARK 3 T11: 0.1916 T22: 0.1912 REMARK 3 T33: 0.1846 T12: -0.0070 REMARK 3 T13: 0.0332 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 3.4048 L22: 0.1586 REMARK 3 L33: 1.3283 L12: 0.5526 REMARK 3 L13: 1.9879 L23: 0.4760 REMARK 3 S TENSOR REMARK 3 S11: 0.1258 S12: -0.4320 S13: -0.1236 REMARK 3 S21: 0.0486 S22: -0.1332 S23: 0.0670 REMARK 3 S31: 0.1560 S32: -0.2562 S33: -0.0256 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9901 18.6150 -7.5568 REMARK 3 T TENSOR REMARK 3 T11: 0.1943 T22: 0.1901 REMARK 3 T33: 0.2037 T12: 0.0256 REMARK 3 T13: -0.0008 T23: 0.0423 REMARK 3 L TENSOR REMARK 3 L11: 3.3354 L22: 2.0567 REMARK 3 L33: 2.2281 L12: 0.2932 REMARK 3 L13: -0.2401 L23: 0.6629 REMARK 3 S TENSOR REMARK 3 S11: -0.0262 S12: -0.2988 S13: -0.2320 REMARK 3 S21: 0.2387 S22: 0.0157 S23: -0.1306 REMARK 3 S31: 0.2662 S32: 0.0162 S33: 0.0110 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.1228 27.8574 -16.9502 REMARK 3 T TENSOR REMARK 3 T11: 0.1711 T22: 0.1742 REMARK 3 T33: 0.2445 T12: 0.0124 REMARK 3 T13: -0.0050 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 3.8617 L22: 3.3082 REMARK 3 L33: 2.2002 L12: 0.1265 REMARK 3 L13: -0.5437 L23: -0.2442 REMARK 3 S TENSOR REMARK 3 S11: 0.0032 S12: 0.2378 S13: 0.3893 REMARK 3 S21: -0.1425 S22: 0.1753 S23: 0.2257 REMARK 3 S31: -0.2293 S32: -0.1640 S33: -0.2239 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 8IFR 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_1300035596. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-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 : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36606 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 54.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 1.36700 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 (%): 45.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 21 21 2 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 22.79100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.85350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.79100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.85350 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24380 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 63.70700 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 582 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 684 LIES ON A SPECIAL POSITION. 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 GLN A 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 ASP A 48 CG OD1 OD2 REMARK 470 ARG A 60 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 72 CG OD1 ND2 REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 ASP A 153 CG OD1 OD2 REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR A 169 OG1 CG2 REMARK 470 ASP A 229 CG OD1 OD2 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 C11 P0O A 401 1.77 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 -128.29 52.04 REMARK 500 ASN A 51 69.37 -161.55 REMARK 500 ASN A 84 -121.61 54.78 REMARK 500 TYR A 154 -104.08 54.66 REMARK 500 THR A 169 27.64 83.34 REMARK 500 PRO A 184 49.78 -86.22 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 722 DISTANCE = 5.83 ANGSTROMS DBREF 8IFR A 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 HET P0O A 401 39 HETNAM P0O (1R,2S,5S)-3-[(2S)-2-(TERT-BUTYLCARBAMOYLAMINO)-3,3- HETNAM 2 P0O DIMETHYL-BUTANOYL]-6,6-DIMETHYL-N-[(2S)-5- HETNAM 3 P0O OXIDANYLIDENE-1-[(3S)-2-OXIDANYLIDENEPYRROLIDIN-3- HETNAM 4 P0O YL]HEX-3-EN-2-YL]-3-AZABICYCLO[3.1.0]HEXANE-2- HETNAM 5 P0O CARBOXAMIDE FORMUL 2 P0O C29 H47 N5 O5 FORMUL 3 HOH *222(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 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 LYS A 61 HIS A 64 5 4 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 GLY A 302 1 11 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 VAL A 35 N LEU A 32 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 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 LEU A 167 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 LEU A 167 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 VAL A 171 THR A 175 -1 O VAL A 171 N LEU A 167 CRYST1 45.582 63.707 105.502 90.00 90.00 90.00 P 21 21 2 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 0.021938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009478 0.00000