HEADER VIRAL PROTEIN 23-MAY-23 8P55 TITLE CRYSTAL STRUCTURE OF THE MAIN PROTEASE (3CLPRO/MPRO) OF SARS-COV-2 TITLE 2 OBTAINED IN PRESENCE OF 75 MICROMOLAR MG-132. 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 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, MPRO, 3CLPRO, EXSCALATE4COV, DRUG DISCOVERY, ELETTRA, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.COSTANZI,N.DEMITRI,P.STORICI REVDAT 2 13-NOV-24 8P55 1 REMARK REVDAT 1 01-MAY-24 8P55 0 JRNL AUTH S.ALBANI,E.COSTANZI,G.L.HOANG,M.KUZIKOV,M.FRINGS,N.ANSARI, JRNL AUTH 2 N.DEMITRI,T.T.NGUYEN,V.RIZZI,J.B.SCHULZ,C.BOLM,A.ZALIANI, JRNL AUTH 3 P.CARLONI,P.STORICI,G.ROSSETTI JRNL TITL UNEXPECTED SINGLE-LIGAND OCCUPANCY AND NEGATIVE JRNL TITL 2 COOPERATIVITY IN THE SARS-COV-2 MAIN PROTEASE. JRNL REF J.CHEM.INF.MODEL. V. 64 892 2024 JRNL REFN ESSN 1549-960X JRNL PMID 38051605 JRNL DOI 10.1021/ACS.JCIM.3C01497 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 60314 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 2931 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 41.1900 - 5.1100 0.96 2851 139 0.1770 0.2065 REMARK 3 2 5.1100 - 4.0600 0.98 2752 156 0.1302 0.1612 REMARK 3 3 4.0600 - 3.5500 0.98 2697 193 0.1479 0.1807 REMARK 3 4 3.5500 - 3.2200 0.99 2761 135 0.1549 0.1983 REMARK 3 5 3.2200 - 2.9900 0.99 2763 134 0.1644 0.2083 REMARK 3 6 2.9900 - 2.8100 0.99 2723 136 0.1642 0.1893 REMARK 3 7 2.8100 - 2.6700 1.00 2780 129 0.1598 0.1800 REMARK 3 8 2.6700 - 2.5600 1.00 2749 148 0.1649 0.1867 REMARK 3 9 2.5600 - 2.4600 1.00 2744 118 0.1635 0.2166 REMARK 3 10 2.4600 - 2.3700 1.00 2756 127 0.1683 0.2360 REMARK 3 11 2.3700 - 2.3000 1.00 2691 173 0.1585 0.2112 REMARK 3 12 2.3000 - 2.2300 0.99 2700 147 0.1670 0.2102 REMARK 3 13 2.2300 - 2.1800 0.99 2736 118 0.1673 0.1730 REMARK 3 14 2.1800 - 2.1200 0.99 2705 138 0.1665 0.2043 REMARK 3 15 2.1200 - 2.0700 1.00 2748 115 0.1779 0.2296 REMARK 3 16 2.0700 - 2.0300 1.00 2722 145 0.2014 0.2421 REMARK 3 17 2.0300 - 1.9900 1.00 2692 135 0.2025 0.2306 REMARK 3 18 1.9900 - 1.9500 1.00 2730 133 0.2001 0.2577 REMARK 3 19 1.9500 - 1.9200 0.99 2709 130 0.2205 0.2645 REMARK 3 20 1.9200 - 1.8800 1.00 2711 136 0.2384 0.2538 REMARK 3 21 1.8800 - 1.8500 0.99 2663 146 0.2553 0.3015 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.374 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.52 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 : 0.012 4886 REMARK 3 ANGLE : 1.018 6639 REMARK 3 CHIRALITY : 0.059 749 REMARK 3 PLANARITY : 0.010 863 REMARK 3 DIHEDRAL : 13.780 1750 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1689 -7.3859 -18.3772 REMARK 3 T TENSOR REMARK 3 T11: 0.1473 T22: 0.1613 REMARK 3 T33: 0.1552 T12: 0.0454 REMARK 3 T13: 0.0034 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 2.4841 L22: 0.6688 REMARK 3 L33: 1.8296 L12: 0.1936 REMARK 3 L13: -0.6510 L23: 0.2684 REMARK 3 S TENSOR REMARK 3 S11: -0.0718 S12: -0.0819 S13: -0.0235 REMARK 3 S21: 0.0468 S22: 0.0254 S23: -0.0152 REMARK 3 S31: 0.0501 S32: 0.2125 S33: 0.0422 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.8993 -6.3103 -24.7885 REMARK 3 T TENSOR REMARK 3 T11: 0.1764 T22: 0.3183 REMARK 3 T33: 0.2194 T12: 0.0611 REMARK 3 T13: 0.0094 T23: 0.0161 REMARK 3 L TENSOR REMARK 3 L11: 2.5201 L22: 0.8432 REMARK 3 L33: 3.1242 L12: 0.2918 REMARK 3 L13: -0.6800 L23: -1.0944 REMARK 3 S TENSOR REMARK 3 S11: -0.0357 S12: -0.3091 S13: -0.0178 REMARK 3 S21: 0.1280 S22: -0.0656 S23: -0.0557 REMARK 3 S31: -0.2163 S32: 0.2694 S33: 0.1057 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7143 -16.4245 -21.1358 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.1454 REMARK 3 T33: 0.2193 T12: 0.0474 REMARK 3 T13: 0.0623 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 3.0755 L22: 1.5714 REMARK 3 L33: 4.0184 L12: -1.4659 REMARK 3 L13: 1.8864 L23: -1.6093 REMARK 3 S TENSOR REMARK 3 S11: -0.1750 S12: -0.1859 S13: -0.1505 REMARK 3 S21: 0.0440 S22: -0.0870 S23: 0.0049 REMARK 3 S31: 0.2609 S32: 0.1773 S33: 0.1513 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4906 -2.7348 -23.5872 REMARK 3 T TENSOR REMARK 3 T11: 0.1434 T22: 0.1737 REMARK 3 T33: 0.2005 T12: 0.0011 REMARK 3 T13: 0.0032 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.3871 L22: 0.7942 REMARK 3 L33: 2.0844 L12: -0.0677 REMARK 3 L13: -0.1467 L23: 0.5233 REMARK 3 S TENSOR REMARK 3 S11: 0.0580 S12: 0.0188 S13: -0.0028 REMARK 3 S21: 0.0401 S22: -0.0412 S23: -0.0382 REMARK 3 S31: 0.0165 S32: 0.1307 S33: -0.0091 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9392 -4.3724 -29.3166 REMARK 3 T TENSOR REMARK 3 T11: 0.1181 T22: 0.1460 REMARK 3 T33: 0.1500 T12: 0.0164 REMARK 3 T13: -0.0032 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 3.3141 L22: 0.8189 REMARK 3 L33: 2.4016 L12: 0.0707 REMARK 3 L13: -0.7331 L23: 0.1062 REMARK 3 S TENSOR REMARK 3 S11: 0.0062 S12: 0.2593 S13: 0.0631 REMARK 3 S21: 0.0070 S22: -0.0125 S23: -0.0292 REMARK 3 S31: -0.0456 S32: 0.0822 S33: 0.0076 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9293 -7.6908 -32.3669 REMARK 3 T TENSOR REMARK 3 T11: 0.1331 T22: 0.1928 REMARK 3 T33: 0.1653 T12: 0.0043 REMARK 3 T13: -0.0009 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.6824 L22: 1.1649 REMARK 3 L33: 1.6914 L12: -0.3034 REMARK 3 L13: 0.4254 L23: -0.1723 REMARK 3 S TENSOR REMARK 3 S11: -0.0141 S12: -0.1177 S13: -0.0263 REMARK 3 S21: 0.0618 S22: 0.0292 S23: 0.0499 REMARK 3 S31: -0.0445 S32: -0.0420 S33: -0.0209 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.0999 -10.7632 -1.4049 REMARK 3 T TENSOR REMARK 3 T11: 0.1793 T22: 0.1038 REMARK 3 T33: 0.1547 T12: 0.0211 REMARK 3 T13: 0.0006 T23: -0.0052 REMARK 3 L TENSOR REMARK 3 L11: 2.0252 L22: 1.1716 REMARK 3 L33: 2.9369 L12: -0.3985 REMARK 3 L13: -0.4266 L23: -0.4472 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.1030 S13: -0.2325 REMARK 3 S21: 0.0023 S22: -0.0443 S23: 0.0225 REMARK 3 S31: 0.2852 S32: 0.1002 S33: 0.0527 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.0948 -13.5379 8.5384 REMARK 3 T TENSOR REMARK 3 T11: 0.2750 T22: 0.1845 REMARK 3 T33: 0.2048 T12: -0.0057 REMARK 3 T13: -0.0011 T23: 0.0501 REMARK 3 L TENSOR REMARK 3 L11: 2.9564 L22: 2.6820 REMARK 3 L33: 3.2294 L12: -1.0766 REMARK 3 L13: 0.4031 L23: -0.2707 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: -0.3463 S13: -0.5105 REMARK 3 S21: 0.0184 S22: 0.0303 S23: 0.3342 REMARK 3 S31: 0.6343 S32: -0.1663 S33: 0.0227 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.4625 -2.8068 -4.0896 REMARK 3 T TENSOR REMARK 3 T11: 0.1241 T22: 0.1082 REMARK 3 T33: 0.1420 T12: -0.0073 REMARK 3 T13: -0.0051 T23: 0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.6820 L22: 1.5405 REMARK 3 L33: 2.3465 L12: -0.7701 REMARK 3 L13: -0.3997 L23: -0.3235 REMARK 3 S TENSOR REMARK 3 S11: 0.0327 S12: 0.0110 S13: -0.0510 REMARK 3 S21: -0.0151 S22: -0.0140 S23: 0.0435 REMARK 3 S31: 0.0446 S32: -0.1535 S33: -0.0104 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 201 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.7130 21.5169 -17.0194 REMARK 3 T TENSOR REMARK 3 T11: 0.2852 T22: 0.1596 REMARK 3 T33: 0.1923 T12: 0.0136 REMARK 3 T13: 0.0866 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.9359 L22: 3.2578 REMARK 3 L33: 1.5406 L12: 0.2762 REMARK 3 L13: 0.5089 L23: -1.8887 REMARK 3 S TENSOR REMARK 3 S11: 0.1799 S12: 0.0082 S13: 0.1552 REMARK 3 S21: 0.0895 S22: 0.0045 S23: 0.1019 REMARK 3 S31: -0.5602 S32: -0.0822 S33: -0.1925 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 244 THROUGH 301 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.2345 17.6094 -17.1550 REMARK 3 T TENSOR REMARK 3 T11: 0.3279 T22: 0.1851 REMARK 3 T33: 0.2168 T12: -0.0490 REMARK 3 T13: 0.0623 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 2.4987 L22: 3.6022 REMARK 3 L33: 3.3436 L12: 0.2208 REMARK 3 L13: -1.5853 L23: 0.5976 REMARK 3 S TENSOR REMARK 3 S11: 0.1184 S12: 0.0122 S13: 0.2389 REMARK 3 S21: -0.2034 S22: 0.1581 S23: -0.2752 REMARK 3 S31: -0.7629 S32: 0.2898 S33: -0.1639 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 8P55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-21 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60402 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 67.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.12100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 7BB2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M DIETHYLENE GLYCOL 0.12M REMARK 280 TRIETHYLENE GLYCOL 0.12M TETRAETHYLENE GLYCOL 0.12M REMARK 280 PENTAETHYLENE GLYCOL, 0.1M IMIDAZOLE/MES PH 6.5, 20% V/V REMARK 280 ETHYLENE GLYCOL 10 % W/V PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.81500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.93850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.35200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.93850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.81500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.35200 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: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 GLN B 306 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 -128.85 54.46 REMARK 500 ASN A 51 56.12 -142.29 REMARK 500 ASN A 84 -122.75 50.25 REMARK 500 ASP A 155 9.67 58.13 REMARK 500 ASP B 33 -129.92 52.58 REMARK 500 ASN B 51 74.56 -150.62 REMARK 500 ASN B 84 -125.83 55.51 REMARK 500 TYR B 154 -102.22 62.11 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 861 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 862 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 863 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 864 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 865 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A 866 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 867 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B 756 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B 757 DISTANCE = 6.42 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD2 REMARK 620 2 GLU A 178 OE1 115.5 REMARK 620 3 HOH A 515 O 53.9 74.1 REMARK 620 4 HOH A 774 O 96.4 108.6 144.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 221 O REMARK 620 2 ASN B 221 OD1 74.4 REMARK 620 3 PHE B 223 O 114.9 95.0 REMARK 620 4 ASP B 263 O 153.5 118.1 88.4 REMARK 620 5 ASP B 263 OD1 98.3 172.1 90.8 67.3 REMARK 620 6 HOH B 521 O 81.2 95.8 162.6 74.5 79.8 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: NULL REMARK 630 MOLECULE NAME: N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-1-HYDROXY- REMARK 630 4-METHYLPENTAN-2-YL]-L-LEUCINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 ALD A 402 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU LEU DCL REMARK 630 DETAILS: NULL DBREF 8P55 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 8P55 B 1 306 UNP P0DTD1 R1AB_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 NA A 401 1 HET ALD A 402 76 HET EDO B 401 10 HET DMS B 402 10 HET CL B 403 1 HET NA B 404 1 HETNAM NA SODIUM ION HETNAM ALD N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-1-HYDROXY-4- HETNAM 2 ALD METHYLPENTAN-2-YL]-L-LEUCINAMIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NA 2(NA 1+) FORMUL 4 ALD C26 H43 N3 O5 FORMUL 5 EDO C2 H6 O2 FORMUL 6 DMS C2 H6 O S FORMUL 7 CL CL 1- FORMUL 9 HOH *624(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 ARG A 60 1 8 HELIX 5 AA5 LYS A 61 PHE A 66 5 6 HELIX 6 AA6 ILE A 152 CYS A 156 5 5 HELIX 7 AA7 ILE A 200 ASN A 214 1 15 HELIX 8 AA8 THR A 226 MET A 235 1 10 HELIX 9 AA9 LYS A 236 ASN A 238 5 3 HELIX 10 AB1 THR A 243 LEU A 250 1 8 HELIX 11 AB2 LEU A 250 GLY A 258 1 9 HELIX 12 AB3 ALA A 260 GLY A 275 1 16 HELIX 13 AB4 THR A 292 CYS A 300 1 9 HELIX 14 AB5 SER B 10 GLY B 15 1 6 HELIX 15 AB6 HIS B 41 CYS B 44 5 4 HELIX 16 AB7 THR B 45 ASN B 51 1 7 HELIX 17 AB8 ASN B 53 LYS B 61 1 9 HELIX 18 AB9 SER B 62 PHE B 66 5 5 HELIX 19 AC1 ILE B 200 ASN B 214 1 15 HELIX 20 AC2 THR B 226 TYR B 237 1 12 HELIX 21 AC3 THR B 243 LEU B 250 1 8 HELIX 22 AC4 LEU B 250 GLY B 258 1 9 HELIX 23 AC5 ALA B 260 GLY B 275 1 16 HELIX 24 AC6 THR B 292 GLY B 302 1 11 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 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 SER A 81 O LYS A 88 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 VAL A 157 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASN A 151 -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 VAL A 157 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 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N ALA B 70 O VAL B 73 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N GLN B 19 O GLN B 69 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O GLY B 29 N VAL B 18 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 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -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 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C22 ALD A 402 1555 1555 1.77 LINK OD2 ASP A 176 NA NA A 401 1555 1555 3.05 LINK OE1 GLU A 178 NA NA A 401 1555 1555 2.42 LINK NA NA A 401 O HOH A 515 1555 1555 2.30 LINK NA NA A 401 O HOH A 774 1555 1555 2.39 LINK O ASN B 221 NA NA B 404 1555 1555 2.52 LINK OD1 ASN B 221 NA NA B 404 1555 1555 2.22 LINK O PHE B 223 NA NA B 404 1555 1555 2.28 LINK O ASP B 263 NA NA B 404 1555 1555 3.05 LINK OD1 ASP B 263 NA NA B 404 1555 1555 2.09 LINK NA NA B 404 O HOH B 521 1555 1555 2.39 CRYST1 67.630 100.704 103.877 90.00 90.00 90.00 P 21 21 21 8 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 0.014786 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009930 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009627 0.00000