HEADER VIRAL PROTEIN/INHIBITOR 04-AUG-23 8TPE TITLE SYNTHESIS, X-RAY CRYSTALLOGRAPHIC AND BIOLOGICAL ACTIVITIES OF TITLE 2 COVALENT, NON-PEPTIDIC INHIBITORS OF SARS-COV-2 MAIN PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NSP7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 3 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 4 ORGANISM_TAXID: 2901879; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NON-PEPTIDIC INHIBITORS, INHIBITORS, SARS-COV-2, MAIN PROTEASE, MPRO, KEYWDS 2 VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.K.CHUA,Y.SONG REVDAT 2 21-FEB-24 8TPE 1 JRNL REVDAT 1 24-JAN-24 8TPE 0 JRNL AUTH M.ASHRAF-UZ-ZAMAN,T.K.CHUA,X.LI,Y.YAO,B.K.MOKU,C.B.MISHRA, JRNL AUTH 2 V.AVADHANULA,P.A.PIEDRA,Y.SONG JRNL TITL DESIGN, SYNTHESIS, X-RAY CRYSTALLOGRAPHY, AND BIOLOGICAL JRNL TITL 2 ACTIVITIES OF COVALENT, NON-PEPTIDIC INHIBITORS OF JRNL TITL 3 SARS-COV-2 MAIN PROTEASE. JRNL REF ACS INFECT DIS. V. 10 715 2024 JRNL REFN ESSN 2373-8227 JRNL PMID 38192109 JRNL DOI 10.1021/ACSINFECDIS.3C00565 REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 68646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1921 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 38.4340 - 3.8791 0.97 4842 143 0.1597 0.1782 REMARK 3 2 3.8791 - 3.0794 0.99 4886 139 0.1695 0.2208 REMARK 3 3 3.0794 - 2.6902 0.98 4799 134 0.1985 0.2450 REMARK 3 4 2.6902 - 2.4443 0.99 4854 140 0.2070 0.2553 REMARK 3 5 2.4443 - 2.2691 0.99 4836 140 0.2040 0.2417 REMARK 3 6 2.2691 - 2.1354 0.98 4763 140 0.2088 0.2447 REMARK 3 7 2.1354 - 2.0284 0.99 4818 138 0.2199 0.2627 REMARK 3 8 2.0284 - 1.9401 0.99 4843 138 0.2257 0.2621 REMARK 3 9 1.9401 - 1.8654 0.99 4771 140 0.2622 0.2775 REMARK 3 10 1.8654 - 1.8011 0.98 4751 137 0.2766 0.3115 REMARK 3 11 1.8011 - 1.7448 0.98 4778 141 0.3017 0.3326 REMARK 3 12 1.7448 - 1.6949 0.98 4800 142 0.3146 0.3133 REMARK 3 13 1.6949 - 1.6503 0.97 4687 129 0.3516 0.3403 REMARK 3 14 1.6503 - 1.6100 0.89 4297 120 0.3740 0.3665 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.030 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 4928 REMARK 3 ANGLE : 0.884 6709 REMARK 3 CHIRALITY : 0.052 748 REMARK 3 PLANARITY : 0.006 873 REMARK 3 DIHEDRAL : 8.114 3929 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 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5952 7.4975 41.7986 REMARK 3 T TENSOR REMARK 3 T11: 0.1450 T22: 0.1490 REMARK 3 T33: 0.1243 T12: -0.0253 REMARK 3 T13: 0.0267 T23: 0.0402 REMARK 3 L TENSOR REMARK 3 L11: 1.5580 L22: 2.4825 REMARK 3 L33: 2.1003 L12: 0.6803 REMARK 3 L13: 1.1521 L23: 0.7990 REMARK 3 S TENSOR REMARK 3 S11: -0.0759 S12: 0.2329 S13: 0.1332 REMARK 3 S21: -0.1733 S22: 0.0681 S23: 0.0020 REMARK 3 S31: -0.1277 S32: 0.1879 S33: -0.0071 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.4247 -6.7125 44.2535 REMARK 3 T TENSOR REMARK 3 T11: 0.1519 T22: 0.1330 REMARK 3 T33: 0.1316 T12: -0.0178 REMARK 3 T13: -0.0057 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 3.0141 L22: 1.9500 REMARK 3 L33: 0.7818 L12: 2.0508 REMARK 3 L13: 1.1565 L23: 1.1211 REMARK 3 S TENSOR REMARK 3 S11: 0.1657 S12: 0.0800 S13: -0.2808 REMARK 3 S21: 0.1503 S22: -0.0017 S23: -0.2698 REMARK 3 S31: 0.1271 S32: 0.0176 S33: -0.1448 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.4237 -18.6523 38.4029 REMARK 3 T TENSOR REMARK 3 T11: 0.1277 T22: 0.1524 REMARK 3 T33: 0.1040 T12: -0.0541 REMARK 3 T13: 0.0037 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 3.6555 L22: 2.9196 REMARK 3 L33: 2.9539 L12: -0.4907 REMARK 3 L13: 0.1003 L23: 0.7139 REMARK 3 S TENSOR REMARK 3 S11: -0.1186 S12: 0.2530 S13: -0.0384 REMARK 3 S21: -0.0815 S22: 0.0462 S23: 0.0618 REMARK 3 S31: 0.0636 S32: -0.0904 S33: 0.0605 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8010 8.2392 18.6481 REMARK 3 T TENSOR REMARK 3 T11: 0.2310 T22: 0.2969 REMARK 3 T33: 0.2473 T12: -0.0058 REMARK 3 T13: -0.0391 T23: 0.0604 REMARK 3 L TENSOR REMARK 3 L11: 2.3672 L22: 2.1840 REMARK 3 L33: 4.2072 L12: -0.2630 REMARK 3 L13: 1.8004 L23: 0.2798 REMARK 3 S TENSOR REMARK 3 S11: -0.4345 S12: 0.3015 S13: 0.4365 REMARK 3 S21: -0.0156 S22: 0.0538 S23: 0.1756 REMARK 3 S31: -0.5544 S32: -0.1093 S33: 0.2824 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7766 13.9901 9.9485 REMARK 3 T TENSOR REMARK 3 T11: 0.4506 T22: 0.4725 REMARK 3 T33: 0.4916 T12: 0.0590 REMARK 3 T13: -0.1196 T23: 0.0839 REMARK 3 L TENSOR REMARK 3 L11: 2.8122 L22: 3.6094 REMARK 3 L33: 3.9452 L12: 1.6261 REMARK 3 L13: 2.1294 L23: 0.9995 REMARK 3 S TENSOR REMARK 3 S11: -0.4314 S12: -0.0202 S13: 0.7574 REMARK 3 S21: -0.1336 S22: -0.1169 S23: 0.8048 REMARK 3 S31: -0.5938 S32: -0.4680 S33: 0.5137 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 100 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6837 0.5427 17.1836 REMARK 3 T TENSOR REMARK 3 T11: 0.1454 T22: 0.2800 REMARK 3 T33: 0.2259 T12: -0.0245 REMARK 3 T13: -0.0241 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 2.5814 L22: 4.0638 REMARK 3 L33: 4.8176 L12: -0.6910 REMARK 3 L13: 0.6379 L23: 1.0438 REMARK 3 S TENSOR REMARK 3 S11: -0.0998 S12: 0.4468 S13: 0.1402 REMARK 3 S21: 0.0469 S22: 0.1686 S23: -0.3249 REMARK 3 S31: 0.0191 S32: 0.3047 S33: -0.0835 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 156 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3363 -6.5568 12.2864 REMARK 3 T TENSOR REMARK 3 T11: 0.1872 T22: 0.3917 REMARK 3 T33: 0.2196 T12: -0.0246 REMARK 3 T13: -0.0014 T23: -0.0346 REMARK 3 L TENSOR REMARK 3 L11: 3.3594 L22: 2.2826 REMARK 3 L33: 2.0930 L12: -1.7543 REMARK 3 L13: 1.1690 L23: -0.4422 REMARK 3 S TENSOR REMARK 3 S11: 0.1192 S12: 0.5092 S13: -0.2517 REMARK 3 S21: -0.2542 S22: 0.0065 S23: 0.1964 REMARK 3 S31: 0.0534 S32: 0.1579 S33: -0.1574 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 214 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.0045 -25.0857 16.1200 REMARK 3 T TENSOR REMARK 3 T11: 0.5058 T22: 0.7967 REMARK 3 T33: 0.7190 T12: 0.2968 REMARK 3 T13: -0.1488 T23: -0.3340 REMARK 3 L TENSOR REMARK 3 L11: 3.8407 L22: 0.1004 REMARK 3 L33: 0.5724 L12: 0.1643 REMARK 3 L13: -0.5174 L23: -0.1658 REMARK 3 S TENSOR REMARK 3 S11: 0.0987 S12: 0.1188 S13: -0.9161 REMARK 3 S21: -0.0650 S22: 0.3374 S23: -0.3729 REMARK 3 S31: 0.5072 S32: 0.8290 S33: -0.2442 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 237 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.7237 -15.9873 18.6371 REMARK 3 T TENSOR REMARK 3 T11: 0.2591 T22: 0.5807 REMARK 3 T33: 0.3406 T12: 0.0993 REMARK 3 T13: -0.0353 T23: -0.1687 REMARK 3 L TENSOR REMARK 3 L11: 4.3226 L22: 1.5251 REMARK 3 L33: 3.4148 L12: 0.6907 REMARK 3 L13: 0.2652 L23: 0.1715 REMARK 3 S TENSOR REMARK 3 S11: -0.0951 S12: 0.1358 S13: -0.3449 REMARK 3 S21: 0.0810 S22: 0.3064 S23: -0.1954 REMARK 3 S31: 0.2570 S32: 0.6227 S33: -0.2360 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 8TPE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276157. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-23 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71237 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.22100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 2.52500 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 200MM NACL, 100MM REMARK 280 HEPES/NAOH PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.03200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 750 O HOH B 785 1.84 REMARK 500 O HOH A 828 O HOH A 859 1.89 REMARK 500 O HOH A 774 O HOH A 815 1.91 REMARK 500 NH1 ARG B 298 O HOH B 601 1.98 REMARK 500 OD1 ASP A 92 O HOH A 601 2.00 REMARK 500 O HOH A 835 O HOH A 837 2.03 REMARK 500 O HOH A 799 O HOH A 811 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 780 O HOH A 846 1565 1.94 REMARK 500 O HOH B 752 O HOH B 794 1565 2.11 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 -132.40 52.92 REMARK 500 ASN A 51 77.11 -156.45 REMARK 500 ASN A 84 -121.68 54.20 REMARK 500 TYR A 154 -96.25 44.25 REMARK 500 ASP B 33 -131.02 52.72 REMARK 500 ASN B 51 80.17 -155.47 REMARK 500 ASN B 84 -121.88 54.01 REMARK 500 TYR B 154 -102.96 49.76 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 877 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 878 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH B 811 DISTANCE = 6.58 ANGSTROMS DBREF 8TPE A 1 305 UNP P0DTD1 R1AB_SARS2 3264 3568 DBREF 8TPE B 1 305 UNP P0DTD1 R1AB_SARS2 3264 3568 SEQRES 1 A 305 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 A 305 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 A 305 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 A 305 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 A 305 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 A 305 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 A 305 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 A 305 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 A 305 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 A 305 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 A 305 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 A 305 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 A 305 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 A 305 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 A 305 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 A 305 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 A 305 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 A 305 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 A 305 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 A 305 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 A 305 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 A 305 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 A 305 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 A 305 CYS SER GLY VAL THR PHE SEQRES 1 B 305 SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY LYS VAL SEQRES 2 B 305 GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR THR THR SEQRES 3 B 305 LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR CYS PRO SEQRES 4 B 305 ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU ASN PRO SEQRES 5 B 305 ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN HIS ASN SEQRES 6 B 305 PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG VAL ILE SEQRES 7 B 305 GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU LYS VAL SEQRES 8 B 305 ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS PHE VAL SEQRES 9 B 305 ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU ALA CYS SEQRES 10 B 305 TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS ALA MET SEQRES 11 B 305 ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU ASN GLY SEQRES 12 B 305 SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR ASP CYS SEQRES 13 B 305 VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU PRO THR SEQRES 14 B 305 GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN PHE TYR SEQRES 15 B 305 GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA ALA GLY SEQRES 16 B 305 THR ASP THR THR ILE THR VAL ASN VAL LEU ALA TRP LEU SEQRES 17 B 305 TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE LEU ASN SEQRES 18 B 305 ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU VAL ALA SEQRES 19 B 305 MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP HIS VAL SEQRES 20 B 305 ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY ILE ALA SEQRES 21 B 305 VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU LEU GLN SEQRES 22 B 305 ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER ALA LEU SEQRES 23 B 305 LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL ARG GLN SEQRES 24 B 305 CYS SER GLY VAL THR PHE HET JK0 A 500 33 HET JK0 B 500 33 HETNAM JK0 N-[(1R)-2-(BENZYLAMINO)-2-OXO-1-(PYRIDIN-3-YL)ETHYL]-N- HETNAM 2 JK0 (4-TERT-BUTYLPHENYL)-3-HYDROXYPROPANAMIDE FORMUL 3 JK0 2(C27 H31 N3 O3) FORMUL 5 HOH *489(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 ASN A 53 ARG A 60 1 8 HELIX 4 AA4 SER A 62 HIS A 64 5 3 HELIX 5 AA5 ILE A 200 ASN A 214 1 15 HELIX 6 AA6 THR A 226 TYR A 237 1 12 HELIX 7 AA7 THR A 243 LEU A 250 1 8 HELIX 8 AA8 LEU A 250 GLY A 258 1 9 HELIX 9 AA9 ALA A 260 GLY A 275 1 16 HELIX 10 AB1 THR A 292 GLY A 302 1 11 HELIX 11 AB2 SER B 10 GLY B 15 1 6 HELIX 12 AB3 HIS B 41 CYS B 44 5 4 HELIX 13 AB4 ASN B 53 ARG B 60 1 8 HELIX 14 AB5 SER B 62 HIS B 64 5 3 HELIX 15 AB6 ILE B 200 ASN B 214 1 15 HELIX 16 AB7 THR B 226 TYR B 237 1 12 HELIX 17 AB8 THR B 243 LEU B 250 1 8 HELIX 18 AB9 LEU B 250 GLY B 258 1 9 HELIX 19 AC1 ALA B 260 GLY B 275 1 16 HELIX 20 AC2 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 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASP A 153 O CYS A 156 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N 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 ILE B 78 O LYS B 90 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 SG CYS A 145 C06 JK0 A 500 1555 1555 1.78 LINK SG CYS B 145 C06 JK0 B 500 1555 1555 1.78 CRYST1 44.743 54.064 115.330 90.00 101.00 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022350 0.000000 0.004344 0.00000 SCALE2 0.000000 0.018497 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008833 0.00000