HEADER VIRAL PROTEIN 23-MAY-23 8P58 TITLE CRYSTAL STRUCTURE OF THE MAIN PROTEASE (3CLPRO/MPRO) OF SARS-COV-2 TITLE 2 OBTAINED IN PRESENCE OF 500 MICROMOLAR X77 ENANTIOMER R. 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 8P58 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 104034 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5304 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 49.4800 - 4.8200 1.00 3551 171 0.1692 0.1741 REMARK 3 2 4.8100 - 3.8200 1.00 3402 178 0.1303 0.1241 REMARK 3 3 3.8200 - 3.3400 1.00 3358 181 0.1473 0.1651 REMARK 3 4 3.3400 - 3.0300 1.00 3357 167 0.1513 0.1798 REMARK 3 5 3.0300 - 2.8200 1.00 3316 172 0.1451 0.1571 REMARK 3 6 2.8200 - 2.6500 1.00 3318 175 0.1468 0.1679 REMARK 3 7 2.6500 - 2.5200 1.00 3288 195 0.1473 0.1889 REMARK 3 8 2.5200 - 2.4100 1.00 3308 175 0.1495 0.1689 REMARK 3 9 2.4100 - 2.3200 1.00 3253 203 0.1401 0.1921 REMARK 3 10 2.3200 - 2.2400 1.00 3300 191 0.1409 0.1497 REMARK 3 11 2.2400 - 2.1700 1.00 3259 174 0.1397 0.1593 REMARK 3 12 2.1700 - 2.1000 1.00 3277 185 0.1428 0.1429 REMARK 3 13 2.1000 - 2.0500 1.00 3262 194 0.1461 0.1821 REMARK 3 14 2.0500 - 2.0000 1.00 3258 203 0.1511 0.1937 REMARK 3 15 2.0000 - 1.9500 1.00 3280 180 0.1585 0.1830 REMARK 3 16 1.9500 - 1.9100 1.00 3280 176 0.1666 0.2029 REMARK 3 17 1.9100 - 1.8700 1.00 3241 177 0.1773 0.2261 REMARK 3 18 1.8700 - 1.8400 1.00 3236 191 0.1854 0.2208 REMARK 3 19 1.8400 - 1.8000 1.00 3272 198 0.1865 0.2401 REMARK 3 20 1.8000 - 1.7700 1.00 3244 176 0.1872 0.2259 REMARK 3 21 1.7700 - 1.7500 1.00 3287 156 0.1920 0.2408 REMARK 3 22 1.7500 - 1.7200 1.00 3279 183 0.1958 0.2914 REMARK 3 23 1.7200 - 1.6900 1.00 3241 157 0.2011 0.2440 REMARK 3 24 1.6900 - 1.6700 1.00 3288 157 0.2091 0.2282 REMARK 3 25 1.6700 - 1.6500 1.00 3286 146 0.2250 0.2360 REMARK 3 26 1.6500 - 1.6300 1.00 3264 175 0.2337 0.2368 REMARK 3 27 1.6300 - 1.6100 1.00 3253 175 0.2561 0.3051 REMARK 3 28 1.6100 - 1.5900 1.00 3252 164 0.2713 0.2834 REMARK 3 29 1.5900 - 1.5700 1.00 3257 165 0.2706 0.3153 REMARK 3 30 1.5700 - 1.5500 1.00 3263 164 0.2666 0.2618 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) : 0.156 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.702 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.22 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 5049 REMARK 3 ANGLE : 1.183 6860 REMARK 3 CHIRALITY : 0.067 769 REMARK 3 PLANARITY : 0.010 891 REMARK 3 DIHEDRAL : 13.820 1841 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 12 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1569 -7.0393 -18.7012 REMARK 3 T TENSOR REMARK 3 T11: 0.1491 T22: 0.1579 REMARK 3 T33: 0.1519 T12: 0.0133 REMARK 3 T13: -0.0029 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.3743 L22: 0.4838 REMARK 3 L33: 1.3939 L12: -0.2398 REMARK 3 L13: -0.6841 L23: 0.0211 REMARK 3 S TENSOR REMARK 3 S11: -0.0761 S12: -0.0712 S13: 0.0165 REMARK 3 S21: 0.0392 S22: 0.0235 S23: -0.0355 REMARK 3 S31: 0.0119 S32: 0.1589 S33: 0.0658 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.0290 -5.7247 -25.0168 REMARK 3 T TENSOR REMARK 3 T11: 0.1417 T22: 0.2716 REMARK 3 T33: 0.1982 T12: 0.0312 REMARK 3 T13: -0.0025 T23: 0.0263 REMARK 3 L TENSOR REMARK 3 L11: 2.1490 L22: 0.8922 REMARK 3 L33: 2.4869 L12: 0.2231 REMARK 3 L13: -1.3961 L23: -0.9728 REMARK 3 S TENSOR REMARK 3 S11: -0.0509 S12: -0.2998 S13: -0.0653 REMARK 3 S21: 0.0826 S22: -0.0286 S23: -0.0969 REMARK 3 S31: -0.1201 S32: 0.3225 S33: 0.0800 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.8617 -16.0930 -21.6171 REMARK 3 T TENSOR REMARK 3 T11: 0.1789 T22: 0.1303 REMARK 3 T33: 0.2059 T12: 0.0218 REMARK 3 T13: 0.0289 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 3.2697 L22: 1.5234 REMARK 3 L33: 4.8373 L12: -1.6480 REMARK 3 L13: 2.3272 L23: -1.7315 REMARK 3 S TENSOR REMARK 3 S11: -0.0680 S12: 0.0069 S13: -0.2550 REMARK 3 S21: 0.0465 S22: -0.0050 S23: 0.0228 REMARK 3 S31: 0.1520 S32: 0.3180 S33: -0.0032 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 139 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4979 -2.4815 -23.9447 REMARK 3 T TENSOR REMARK 3 T11: 0.1545 T22: 0.1309 REMARK 3 T33: 0.1910 T12: 0.0006 REMARK 3 T13: 0.0043 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.4076 L22: 0.6371 REMARK 3 L33: 2.6312 L12: 0.5372 REMARK 3 L13: 0.6151 L23: 0.6586 REMARK 3 S TENSOR REMARK 3 S11: 0.0146 S12: 0.0164 S13: 0.1510 REMARK 3 S21: 0.0370 S22: -0.0361 S23: -0.0035 REMARK 3 S31: -0.0543 S32: 0.0729 S33: 0.0352 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 140 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7587 -4.6395 -29.5562 REMARK 3 T TENSOR REMARK 3 T11: 0.1526 T22: 0.1305 REMARK 3 T33: 0.1510 T12: 0.0031 REMARK 3 T13: 0.0049 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 3.4149 L22: 0.3215 REMARK 3 L33: 0.8253 L12: -0.0103 REMARK 3 L13: 0.2147 L23: -0.1759 REMARK 3 S TENSOR REMARK 3 S11: -0.0112 S12: 0.2574 S13: 0.1486 REMARK 3 S21: -0.0349 S22: -0.0127 S23: -0.0454 REMARK 3 S31: -0.0235 S32: 0.0589 S33: 0.0056 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 274 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.1369 -8.2099 -37.5122 REMARK 3 T TENSOR REMARK 3 T11: 0.1419 T22: 0.1870 REMARK 3 T33: 0.1586 T12: 0.0052 REMARK 3 T13: -0.0185 T23: -0.0108 REMARK 3 L TENSOR REMARK 3 L11: 1.3240 L22: 1.4082 REMARK 3 L33: 1.3108 L12: -0.1399 REMARK 3 L13: 0.2878 L23: -0.2844 REMARK 3 S TENSOR REMARK 3 S11: 0.0190 S12: 0.0026 S13: -0.0930 REMARK 3 S21: -0.0636 S22: -0.0058 S23: 0.0267 REMARK 3 S31: 0.0376 S32: 0.0407 S33: -0.0123 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 275 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0431 -5.7451 -24.6796 REMARK 3 T TENSOR REMARK 3 T11: 0.1591 T22: 0.2545 REMARK 3 T33: 0.1812 T12: -0.0112 REMARK 3 T13: 0.0117 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.7662 L22: 4.2479 REMARK 3 L33: 3.0009 L12: -1.9805 REMARK 3 L13: 0.8885 L23: -0.1871 REMARK 3 S TENSOR REMARK 3 S11: -0.1074 S12: -0.2560 S13: -0.1742 REMARK 3 S21: 0.2780 S22: 0.1799 S23: 0.3786 REMARK 3 S31: -0.0722 S32: -0.2336 S33: -0.0361 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.2852 -10.8119 -1.9360 REMARK 3 T TENSOR REMARK 3 T11: 0.1968 T22: 0.1269 REMARK 3 T33: 0.1739 T12: -0.0006 REMARK 3 T13: 0.0104 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 1.4584 L22: 0.6104 REMARK 3 L33: 2.4263 L12: -0.0690 REMARK 3 L13: -0.6057 L23: -0.6083 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: -0.1293 S13: -0.1652 REMARK 3 S21: -0.0016 S22: -0.0526 S23: -0.0146 REMARK 3 S31: 0.2181 S32: 0.0828 S33: 0.0956 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.3436 -13.8026 7.9579 REMARK 3 T TENSOR REMARK 3 T11: 0.2356 T22: 0.1876 REMARK 3 T33: 0.1820 T12: -0.0195 REMARK 3 T13: 0.0014 T23: 0.0589 REMARK 3 L TENSOR REMARK 3 L11: 2.7786 L22: 1.9049 REMARK 3 L33: 2.6144 L12: -0.4866 REMARK 3 L13: -0.1920 L23: -0.4321 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: -0.3556 S13: -0.5082 REMARK 3 S21: 0.1328 S22: 0.0528 S23: 0.1700 REMARK 3 S31: 0.4393 S32: -0.1301 S33: 0.0137 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 111 THROUGH 200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5006 -2.8498 -4.5130 REMARK 3 T TENSOR REMARK 3 T11: 0.1285 T22: 0.1058 REMARK 3 T33: 0.1119 T12: -0.0058 REMARK 3 T13: -0.0005 T23: 0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.7494 L22: 1.3440 REMARK 3 L33: 2.0226 L12: -0.4091 REMARK 3 L13: -0.4934 L23: -0.3753 REMARK 3 S TENSOR REMARK 3 S11: 0.0424 S12: 0.0106 S13: -0.0380 REMARK 3 S21: -0.0194 S22: -0.0289 S23: 0.0131 REMARK 3 S31: -0.0003 S32: -0.1183 S33: -0.0016 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 201 THROUGH 243 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.6809 21.6980 -16.9674 REMARK 3 T TENSOR REMARK 3 T11: 0.2843 T22: 0.1354 REMARK 3 T33: 0.1959 T12: 0.0374 REMARK 3 T13: 0.0785 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.8991 L22: 4.1316 REMARK 3 L33: 1.0530 L12: 0.6564 REMARK 3 L13: 0.3728 L23: -1.8098 REMARK 3 S TENSOR REMARK 3 S11: 0.2260 S12: 0.0231 S13: 0.2628 REMARK 3 S21: 0.2799 S22: -0.0102 S23: 0.0161 REMARK 3 S31: -0.5384 S32: -0.1203 S33: -0.1648 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 244 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.6704 17.7357 -16.2036 REMARK 3 T TENSOR REMARK 3 T11: 0.2900 T22: 0.1654 REMARK 3 T33: 0.2147 T12: -0.0433 REMARK 3 T13: 0.0171 T23: -0.0387 REMARK 3 L TENSOR REMARK 3 L11: 3.0324 L22: 2.9737 REMARK 3 L33: 2.6049 L12: -0.7003 REMARK 3 L13: -1.3902 L23: -0.2424 REMARK 3 S TENSOR REMARK 3 S11: 0.0252 S12: -0.0730 S13: 0.2594 REMARK 3 S21: 0.0793 S22: 0.0946 S23: -0.3209 REMARK 3 S31: -0.5307 S32: 0.2318 S33: -0.1258 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 8P58 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-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) : 0.9718 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 : 104143 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 104.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 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 (%): 53.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 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 TRIS/BICINE PH 8.5, 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 33.84400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.16450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.41400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.16450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.84400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.41400 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: 5050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 -131.71 53.23 REMARK 500 ASN A 51 57.12 -141.51 REMARK 500 ASN A 84 -124.36 56.41 REMARK 500 ASP A 155 18.83 58.89 REMARK 500 ASP B 33 -131.10 48.46 REMARK 500 ASN B 84 -127.42 53.75 REMARK 500 TYR B 154 -107.71 57.54 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 872 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 873 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH B 788 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH B 789 DISTANCE = 6.68 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 B 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 516 O REMARK 620 2 ASP B 33 OD2 99.6 REMARK 620 3 TYR B 101 OH 81.7 127.2 REMARK 620 4 HOH B 545 O 125.8 129.9 83.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 221 O REMARK 620 2 ASN B 221 OD1 74.5 REMARK 620 3 PHE B 223 O 115.8 92.0 REMARK 620 4 ASP B 263 O 152.9 112.2 90.6 REMARK 620 5 ASP B 263 OD1 102.4 170.5 97.4 66.4 REMARK 620 6 HOH B 522 O 82.6 91.7 161.5 71.3 78.9 REMARK 620 N 1 2 3 4 5 DBREF 8P58 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 8P58 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 EDO A 401 10 HET EDO A 402 10 HET EDO A 403 10 HET EDO A 404 10 HET CL A 405 1 HET X77 A 406 66 HET EDO B 401 10 HET DMS B 402 10 HET EDO B 403 10 HET EDO B 404 10 HET NA B 405 1 HET NA B 406 1 HET CL B 407 1 HET X77 B 408 66 HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETNAM X77 N-(4-TERT-BUTYLPHENYL)-N-[(1R)-2-(CYCLOHEXYLAMINO)-2- HETNAM 2 X77 OXO-1-(PYRIDIN-3-YL)ETHYL]-1H-IMIDAZOLE-4-CARBOXAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 7(C2 H6 O2) FORMUL 7 CL 2(CL 1-) FORMUL 8 X77 2(C27 H33 N5 O2) FORMUL 10 DMS C2 H6 O S FORMUL 13 NA 2(NA 1+) FORMUL 17 HOH *662(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 LYS A 61 HIS A 64 5 4 HELIX 5 AA5 ILE A 152 CYS A 156 5 5 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 MET A 235 1 10 HELIX 8 AA8 LYS A 236 ASN A 238 5 3 HELIX 9 AA9 THR A 243 LEU A 250 1 8 HELIX 10 AB1 LEU A 250 GLY A 258 1 9 HELIX 11 AB2 ALA A 260 GLY A 275 1 16 HELIX 12 AB3 THR A 292 CYS A 300 1 9 HELIX 13 AB4 SER B 10 GLY B 15 1 6 HELIX 14 AB5 HIS B 41 CYS B 44 5 4 HELIX 15 AB6 GLU B 47 ASN B 51 5 5 HELIX 16 AB7 ASN B 53 LYS B 61 1 9 HELIX 17 AB8 SER B 62 HIS B 64 5 3 HELIX 18 AB9 ILE B 200 ASN B 214 1 15 HELIX 19 AC1 THR B 226 TYR B 237 1 12 HELIX 20 AC2 THR B 243 GLY B 258 1 16 HELIX 21 AC3 ALA B 260 GLY B 275 1 16 HELIX 22 AC4 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 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 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 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 GLN B 19 O GLN B 69 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 LYS B 100 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 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 LYS B 100 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK O HOH A 516 NA NA B 406 2555 1555 2.90 LINK OD2 ASP B 33 NA NA B 406 1555 1555 2.27 LINK OH TYR B 101 NA NA B 406 1555 1555 2.56 LINK O ASN B 221 NA NA B 405 1555 1555 2.47 LINK OD1 ASN B 221 NA NA B 405 1555 1555 2.36 LINK O PHE B 223 NA NA B 405 1555 1555 2.26 LINK O ASP B 263 NA NA B 405 1555 1555 3.18 LINK OD1 ASP B 263 NA NA B 405 1555 1555 2.15 LINK NA NA B 405 O HOH B 522 1555 1555 2.49 LINK NA NA B 406 O HOH B 545 1555 1555 2.66 CRYST1 67.688 100.828 104.329 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 0.014774 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009585 0.00000