HEADER VIRAL PROTEIN 23-MAY-23 8P54 TITLE CRYSTAL STRUCTURE OF THE MAIN PROTEASE (3CLPRO/MPRO) OF SARS-COV-2 TITLE 2 OBTAINED IN PRESENCE OF 150 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 1 01-MAY-24 8P54 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. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 93106 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 4580 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 44.9300 - 4.9700 1.00 3139 188 0.1748 0.1903 REMARK 3 2 4.9700 - 3.9500 1.00 3073 146 0.1286 0.1591 REMARK 3 3 3.9500 - 3.4500 1.00 3012 128 0.1512 0.1509 REMARK 3 4 3.4500 - 3.1300 1.00 2995 169 0.1586 0.1714 REMARK 3 5 3.1300 - 2.9100 1.00 3003 141 0.1658 0.1799 REMARK 3 6 2.9100 - 2.7400 1.00 2936 165 0.1614 0.1895 REMARK 3 7 2.7400 - 2.6000 1.00 2962 166 0.1609 0.1708 REMARK 3 8 2.6000 - 2.4900 1.00 2941 171 0.1596 0.1781 REMARK 3 9 2.4900 - 2.3900 1.00 2959 162 0.1590 0.1800 REMARK 3 10 2.3900 - 2.3100 1.00 2890 181 0.1564 0.1718 REMARK 3 11 2.3100 - 2.2400 1.00 2969 151 0.1557 0.1785 REMARK 3 12 2.2400 - 2.1700 1.00 2918 153 0.1539 0.1845 REMARK 3 13 2.1700 - 2.1100 1.00 2926 156 0.1518 0.1785 REMARK 3 14 2.1100 - 2.0600 1.00 2950 147 0.1580 0.1797 REMARK 3 15 2.0600 - 2.0200 1.00 2924 186 0.1611 0.1825 REMARK 3 16 2.0200 - 1.9700 1.00 2942 134 0.1673 0.1770 REMARK 3 17 1.9700 - 1.9300 1.00 2916 151 0.1710 0.1998 REMARK 3 18 1.9300 - 1.9000 1.00 2956 143 0.1872 0.2123 REMARK 3 19 1.9000 - 1.8600 1.00 2967 110 0.1966 0.2127 REMARK 3 20 1.8600 - 1.8300 1.00 2885 170 0.2012 0.2222 REMARK 3 21 1.8300 - 1.8000 1.00 2938 149 0.1987 0.2134 REMARK 3 22 1.8000 - 1.7700 1.00 2913 149 0.1996 0.2213 REMARK 3 23 1.7700 - 1.7500 1.00 2923 146 0.2073 0.2705 REMARK 3 24 1.7500 - 1.7200 1.00 2933 158 0.2126 0.2407 REMARK 3 25 1.7200 - 1.7000 1.00 2928 126 0.2213 0.2422 REMARK 3 26 1.7000 - 1.6800 1.00 2941 136 0.2339 0.2727 REMARK 3 27 1.6800 - 1.6600 1.00 2896 155 0.2523 0.2594 REMARK 3 28 1.6600 - 1.6400 1.00 2944 145 0.2552 0.3200 REMARK 3 29 1.6400 - 1.6200 1.00 2885 145 0.2713 0.3223 REMARK 3 30 1.6200 - 1.6000 1.00 2962 153 0.2775 0.2762 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.083 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.75 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 : 0.010 4893 REMARK 3 ANGLE : 0.974 6650 REMARK 3 CHIRALITY : 0.058 750 REMARK 3 PLANARITY : 0.008 865 REMARK 3 DIHEDRAL : 13.495 1753 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 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.2406 -7.1724 -18.3356 REMARK 3 T TENSOR REMARK 3 T11: 0.1356 T22: 0.1191 REMARK 3 T33: 0.1243 T12: 0.0176 REMARK 3 T13: -0.0010 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 2.5954 L22: 1.1047 REMARK 3 L33: 2.5898 L12: -0.0107 REMARK 3 L13: -0.9351 L23: -0.2899 REMARK 3 S TENSOR REMARK 3 S11: -0.0450 S12: -0.0975 S13: -0.0433 REMARK 3 S21: 0.0370 S22: -0.0143 S23: -0.0443 REMARK 3 S31: 0.0202 S32: 0.2205 S33: 0.0603 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.9936 -6.0271 -24.7507 REMARK 3 T TENSOR REMARK 3 T11: 0.1616 T22: 0.3146 REMARK 3 T33: 0.2172 T12: 0.0274 REMARK 3 T13: 0.0051 T23: 0.0350 REMARK 3 L TENSOR REMARK 3 L11: 2.3240 L22: 0.9068 REMARK 3 L33: 3.5177 L12: 0.1126 REMARK 3 L13: -0.6470 L23: -1.0027 REMARK 3 S TENSOR REMARK 3 S11: -0.0335 S12: -0.2906 S13: -0.0071 REMARK 3 S21: 0.0808 S22: -0.0910 S23: -0.0966 REMARK 3 S31: -0.1132 S32: 0.5085 S33: 0.1311 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8442 -16.2309 -21.1360 REMARK 3 T TENSOR REMARK 3 T11: 0.1750 T22: 0.1281 REMARK 3 T33: 0.1916 T12: 0.0417 REMARK 3 T13: 0.0507 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 2.7747 L22: 1.7042 REMARK 3 L33: 4.9000 L12: -1.1445 REMARK 3 L13: 2.6879 L23: -1.5801 REMARK 3 S TENSOR REMARK 3 S11: -0.0682 S12: 0.0446 S13: -0.1551 REMARK 3 S21: 0.0051 S22: -0.0482 S23: -0.0312 REMARK 3 S31: 0.2764 S32: 0.2936 S33: 0.0002 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.3873 -4.8542 -23.0297 REMARK 3 T TENSOR REMARK 3 T11: 0.1293 T22: 0.1099 REMARK 3 T33: 0.1609 T12: 0.0034 REMARK 3 T13: 0.0036 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 2.6637 L22: 0.9041 REMARK 3 L33: 3.7170 L12: -0.0707 REMARK 3 L13: 0.1740 L23: 0.5291 REMARK 3 S TENSOR REMARK 3 S11: -0.0257 S12: -0.0142 S13: 0.0000 REMARK 3 S21: -0.0009 S22: -0.0356 S23: 0.0006 REMARK 3 S31: -0.0517 S32: 0.0637 S33: 0.0673 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 167 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.5654 -1.3631 -35.1293 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.1840 REMARK 3 T33: 0.1598 T12: -0.0006 REMARK 3 T13: -0.0087 T23: 0.0289 REMARK 3 L TENSOR REMARK 3 L11: 3.0891 L22: 0.5734 REMARK 3 L33: 1.0390 L12: 1.1219 REMARK 3 L13: -0.5341 L23: 0.1842 REMARK 3 S TENSOR REMARK 3 S11: -0.0708 S12: 0.3716 S13: 0.2646 REMARK 3 S21: -0.0797 S22: 0.1019 S23: 0.0692 REMARK 3 S31: -0.1331 S32: -0.0592 S33: -0.0199 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 201 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.8990 -7.5414 -32.3826 REMARK 3 T TENSOR REMARK 3 T11: 0.1365 T22: 0.2168 REMARK 3 T33: 0.1816 T12: 0.0012 REMARK 3 T13: -0.0021 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.2536 L22: 1.7585 REMARK 3 L33: 2.1298 L12: -0.2151 REMARK 3 L13: 0.3738 L23: -0.1461 REMARK 3 S TENSOR REMARK 3 S11: -0.0447 S12: -0.1257 S13: -0.0067 REMARK 3 S21: 0.1002 S22: 0.0573 S23: 0.1371 REMARK 3 S31: -0.0286 S32: -0.1276 S33: -0.0198 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0631 -10.7554 -1.3307 REMARK 3 T TENSOR REMARK 3 T11: 0.1770 T22: 0.1062 REMARK 3 T33: 0.1598 T12: -0.0124 REMARK 3 T13: 0.0014 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.2797 L22: 1.1333 REMARK 3 L33: 2.2693 L12: -0.4841 REMARK 3 L13: 0.4047 L23: -0.5320 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: -0.0748 S13: -0.1522 REMARK 3 S21: -0.0420 S22: 0.0221 S23: 0.1238 REMARK 3 S31: 0.2888 S32: -0.1317 S33: -0.0638 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2845 -7.7126 1.4255 REMARK 3 T TENSOR REMARK 3 T11: 0.1605 T22: 0.1584 REMARK 3 T33: 0.1697 T12: -0.0370 REMARK 3 T13: 0.0237 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 2.0578 L22: 1.2490 REMARK 3 L33: 2.2159 L12: -1.0214 REMARK 3 L13: 0.7948 L23: -0.5024 REMARK 3 S TENSOR REMARK 3 S11: 0.0175 S12: -0.2347 S13: -0.2507 REMARK 3 S21: 0.0495 S22: 0.1000 S23: 0.2009 REMARK 3 S31: 0.2180 S32: -0.3314 S33: -0.0547 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 201 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6937 18.7368 -16.6909 REMARK 3 T TENSOR REMARK 3 T11: 0.2726 T22: 0.1253 REMARK 3 T33: 0.1739 T12: 0.0045 REMARK 3 T13: 0.0606 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 1.5532 L22: 3.2640 REMARK 3 L33: 2.6358 L12: -0.3735 REMARK 3 L13: -1.1728 L23: -0.4406 REMARK 3 S TENSOR REMARK 3 S11: 0.1775 S12: -0.0431 S13: 0.1781 REMARK 3 S21: -0.0136 S22: 0.0196 S23: -0.0253 REMARK 3 S31: -0.4978 S32: 0.0357 S33: -0.1493 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 8P54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130700. 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 : 93197 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 71.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 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 (%): 52.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12M 1,6-HEXANEDIOL 0.12M 1-BUTANOL REMARK 280 0.12M 1,2-PROPANEDIOL 0.12M 2-PROPANOL 0.12M 1,4-BUTANEDIOL REMARK 280 0.12M 1,3-PROPANEDIOL, 0.1 M IMIDAZOLE/MES PH 6.5, 20% V/V PEG REMARK 280 500 MME 10 % W/V PEG 20000, 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 33.87100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.80050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.85950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.80050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.87100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.85950 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: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 -131.30 55.31 REMARK 500 HIS A 41 1.71 -69.81 REMARK 500 ASN A 84 -122.47 52.96 REMARK 500 ASP A 155 14.09 59.85 REMARK 500 ASP B 33 -135.48 54.07 REMARK 500 ASN B 51 74.84 -155.97 REMARK 500 ASN B 84 -124.76 51.69 REMARK 500 TYR B 154 -101.84 58.62 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 = 5.86 ANGSTROMS REMARK 525 HOH A 862 DISTANCE = 6.75 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 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 176 OD2 REMARK 620 2 GLU A 178 OE1 124.9 REMARK 620 3 HOH A 512 O 53.5 87.7 REMARK 620 4 HOH A 767 O 95.2 105.0 146.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 221 O REMARK 620 2 ASN B 221 OD1 73.8 REMARK 620 3 PHE B 223 O 112.5 96.1 REMARK 620 4 ASP B 263 O 153.0 119.9 90.2 REMARK 620 5 ASP B 263 OD1 94.3 168.0 89.2 70.7 REMARK 620 6 HOH B 538 O 77.8 99.4 163.4 76.9 76.7 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 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PHQ LEU LEU DCL REMARK 630 DETAILS: NULL DBREF 8P54 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 8P54 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 ALD A 401 76 HET CL A 402 1 HET NA A 403 1 HET DMS B 401 10 HET EDO B 402 10 HET NA B 403 1 HETNAM ALD N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-1-HYDROXY-4- HETNAM 2 ALD METHYLPENTAN-2-YL]-L-LEUCINAMIDE HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ALD C26 H43 N3 O5 FORMUL 4 CL CL 1- FORMUL 5 NA 2(NA 1+) FORMUL 6 DMS C2 H6 O S FORMUL 7 EDO C2 H6 O2 FORMUL 9 HOH *626(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 SER A 62 HIS A 64 5 3 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 ARG B 60 1 8 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 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 87 N CYS A 38 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 VAL B 68 O LEU B 75 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 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASP B 153 O CYS B 156 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 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 LINK SG CYS A 145 C22 ALD A 401 1555 1555 1.92 LINK OD2 ASP A 176 NA NA A 403 1555 1555 3.03 LINK OE1 GLU A 178 NA NA A 403 1555 1555 2.24 LINK NA NA A 403 O HOH A 512 1555 1555 2.19 LINK NA NA A 403 O HOH A 767 1555 1555 2.49 LINK O ASN B 221 NA NA B 403 1555 1555 2.64 LINK OD1 ASN B 221 NA NA B 403 1555 1555 2.21 LINK O PHE B 223 NA NA B 403 1555 1555 2.31 LINK O ASP B 263 NA NA B 403 1555 1555 2.92 LINK OD1 ASP B 263 NA NA B 403 1555 1555 2.06 LINK NA NA B 403 O HOH B 538 1555 1555 2.37 CRYST1 67.742 99.719 103.601 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 0.014762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009652 0.00000