HEADER VIRAL PROTEIN, HYDROLASE/INHIBITOR 06-AUG-22 8DZ1 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE MUTANT M49I IN COMPLEX TITLE 2 WITH ENSITRELVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICASE POLYPROTEIN 1AB; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MPRO, 3CL, COVID, SARS-COV-2 ENSITRELVIR, NIRMATRELVIR, VIRAL KEYWDS 2 PROTEIN, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.D.NOSKE,G.OLIVA,A.S.GODOY REVDAT 4 25-OCT-23 8DZ1 1 REMARK REVDAT 3 22-MAR-23 8DZ1 1 JRNL REVDAT 2 22-FEB-23 8DZ1 1 JRNL REVDAT 1 05-OCT-22 8DZ1 0 JRNL AUTH G.D.NOSKE,E.DE SOUZA SILVA,M.O.DE GODOY,I.DOLCI, JRNL AUTH 2 R.S.FERNANDES,R.V.C.GUIDO,P.SJO,G.OLIVA,A.S.GODOY JRNL TITL STRUCTURAL BASIS OF NIRMATRELVIR AND ENSITRELVIR ACTIVITY JRNL TITL 2 AGAINST NATURALLY OCCURRING POLYMORPHISMS OF THE SARS-COV-2 JRNL TITL 3 MAIN PROTEASE. JRNL REF J.BIOL.CHEM. V. 299 03004 2023 JRNL REFN ESSN 1083-351X JRNL PMID 36775130 JRNL DOI 10.1016/J.JBC.2023.103004 REMARK 2 REMARK 2 RESOLUTION. 2.08 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 59.2 REMARK 3 NUMBER OF REFLECTIONS : 25093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1300 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 71.5200 - 4.3300 0.98 4628 241 0.1960 0.2284 REMARK 3 2 4.3300 - 3.4400 0.98 4423 245 0.1944 0.2396 REMARK 3 3 3.4300 - 3.0000 0.92 4101 251 0.2286 0.2653 REMARK 3 4 3.0000 - 2.7300 0.81 3596 206 0.2568 0.2895 REMARK 3 5 2.7300 - 2.5300 0.69 3064 155 0.2723 0.3334 REMARK 3 6 2.5300 - 2.3800 0.46 2058 107 0.2804 0.2906 REMARK 3 7 2.3800 - 2.2600 0.25 1084 54 0.2629 0.3505 REMARK 3 8 2.2600 - 2.1600 0.15 681 33 0.2795 0.3341 REMARK 3 9 2.1600 - 2.0800 0.04 158 8 0.2677 0.4250 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.67 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 1:200 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.064 -5.921 23.975 REMARK 3 T TENSOR REMARK 3 T11: 0.1368 T22: 0.1993 REMARK 3 T33: 0.1360 T12: -0.0253 REMARK 3 T13: 0.0020 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 1.9504 L22: 2.0196 REMARK 3 L33: 2.5236 L12: 0.1384 REMARK 3 L13: -0.3745 L23: 0.0288 REMARK 3 S TENSOR REMARK 3 S11: -0.0002 S12: -0.0728 S13: 0.1221 REMARK 3 S21: -0.0256 S22: 0.0087 S23: 0.1274 REMARK 3 S31: 0.1400 S32: -0.3965 S33: 0.0051 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 201:274 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.524 -8.315 36.079 REMARK 3 T TENSOR REMARK 3 T11: 0.1451 T22: 0.2786 REMARK 3 T33: 0.2909 T12: 0.0257 REMARK 3 T13: -0.0174 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.6323 L22: 1.7780 REMARK 3 L33: 2.5596 L12: -0.0387 REMARK 3 L13: 0.2838 L23: 0.0692 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: -0.4030 S13: 0.0160 REMARK 3 S21: 0.1058 S22: -0.1525 S23: -0.2858 REMARK 3 S31: 0.0115 S32: 0.3794 S33: 0.0695 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 275:302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.871 -5.986 24.556 REMARK 3 T TENSOR REMARK 3 T11: 0.2588 T22: 0.3413 REMARK 3 T33: 0.5325 T12: 0.0272 REMARK 3 T13: 0.0306 T23: 0.0242 REMARK 3 L TENSOR REMARK 3 L11: 2.1396 L22: 1.9507 REMARK 3 L33: 3.0231 L12: 0.5286 REMARK 3 L13: -0.1338 L23: -1.0071 REMARK 3 S TENSOR REMARK 3 S11: 0.1360 S12: 1.0559 S13: 0.0619 REMARK 3 S21: -0.5144 S22: -0.0262 S23: -0.7207 REMARK 3 S31: -0.1078 S32: 0.4683 S33: 0.0187 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN B AND RESID 1:43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.047 -10.731 1.415 REMARK 3 T TENSOR REMARK 3 T11: 0.3986 T22: 0.1539 REMARK 3 T33: 0.2037 T12: -0.0202 REMARK 3 T13: 0.0364 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.8021 L22: 0.9291 REMARK 3 L33: 1.4329 L12: 0.1640 REMARK 3 L13: 0.0912 L23: -0.3787 REMARK 3 S TENSOR REMARK 3 S11: -0.0603 S12: 0.3883 S13: -0.0192 REMARK 3 S21: 0.0337 S22: -0.0768 S23: -0.1782 REMARK 3 S31: 1.0010 S32: 0.0004 S33: -0.0340 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN B AND RESID 44:70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.486 -18.660 -10.151 REMARK 3 T TENSOR REMARK 3 T11: 1.0372 T22: 0.7364 REMARK 3 T33: 0.7402 T12: 0.3361 REMARK 3 T13: 0.2047 T23: 0.0339 REMARK 3 L TENSOR REMARK 3 L11: 1.0531 L22: 0.5021 REMARK 3 L33: 0.2386 L12: 0.6526 REMARK 3 L13: 0.1260 L23: 0.1769 REMARK 3 S TENSOR REMARK 3 S11: 0.2662 S12: 0.3775 S13: -0.4171 REMARK 3 S21: -0.6806 S22: -0.3172 S23: -0.9575 REMARK 3 S31: 0.6372 S32: 0.5864 S33: 0.0271 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND RESID 71:120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.769 -9.921 -4.501 REMARK 3 T TENSOR REMARK 3 T11: 0.4299 T22: 0.3588 REMARK 3 T33: 0.2497 T12: 0.0573 REMARK 3 T13: 0.0634 T23: -0.0411 REMARK 3 L TENSOR REMARK 3 L11: 1.2869 L22: 0.7210 REMARK 3 L33: 2.0273 L12: 0.0166 REMARK 3 L13: 0.0910 L23: 0.0568 REMARK 3 S TENSOR REMARK 3 S11: 0.0574 S12: 0.5002 S13: -0.1395 REMARK 3 S21: -0.3793 S22: -0.0535 S23: -0.0523 REMARK 3 S31: 0.5909 S32: 0.1076 S33: 0.0245 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN B AND RESID 121:180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.203 -3.247 4.203 REMARK 3 T TENSOR REMARK 3 T11: 0.2511 T22: 0.2728 REMARK 3 T33: 0.2773 T12: 0.0092 REMARK 3 T13: 0.0866 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 1.5039 L22: 1.4846 REMARK 3 L33: 2.4217 L12: 1.0452 REMARK 3 L13: -0.4345 L23: 0.0606 REMARK 3 S TENSOR REMARK 3 S11: 0.0843 S12: 0.0891 S13: 0.0924 REMARK 3 S21: -0.0566 S22: -0.1833 S23: -0.0565 REMARK 3 S31: 0.1820 S32: 0.3451 S33: 0.0663 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN B AND RESID 181:213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.661 6.616 7.808 REMARK 3 T TENSOR REMARK 3 T11: 0.2736 T22: 0.3167 REMARK 3 T33: 0.3293 T12: -0.0462 REMARK 3 T13: 0.0376 T23: 0.0793 REMARK 3 L TENSOR REMARK 3 L11: 1.3814 L22: 1.3049 REMARK 3 L33: 2.8509 L12: -0.0210 REMARK 3 L13: -0.4259 L23: 0.5863 REMARK 3 S TENSOR REMARK 3 S11: -0.2350 S12: 0.0552 S13: 0.1250 REMARK 3 S21: -0.0410 S22: 0.2704 S23: -0.3648 REMARK 3 S31: 0.2516 S32: 0.7113 S33: 0.0299 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: ( CHAIN B AND RESID 214:250 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.918 22.994 14.697 REMARK 3 T TENSOR REMARK 3 T11: 0.5753 T22: 0.3656 REMARK 3 T33: 0.3958 T12: -0.1776 REMARK 3 T13: 0.0152 T23: 0.0519 REMARK 3 L TENSOR REMARK 3 L11: 0.1585 L22: 1.0632 REMARK 3 L33: 1.4456 L12: 0.0864 REMARK 3 L13: 0.2656 L23: 0.3040 REMARK 3 S TENSOR REMARK 3 S11: -0.2023 S12: 0.2927 S13: 0.1452 REMARK 3 S21: -0.4085 S22: 0.0478 S23: -0.0014 REMARK 3 S31: -0.6967 S32: 0.3235 S33: 0.0742 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: ( CHAIN B AND RESID 251:306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.177 15.612 17.883 REMARK 3 T TENSOR REMARK 3 T11: 0.3253 T22: 0.1663 REMARK 3 T33: 0.3572 T12: 0.0130 REMARK 3 T13: -0.0140 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 1.3839 L22: 2.2570 REMARK 3 L33: 2.5943 L12: -0.2442 REMARK 3 L13: -0.2797 L23: -0.4258 REMARK 3 S TENSOR REMARK 3 S11: -0.0294 S12: -0.1224 S13: 0.0001 REMARK 3 S21: 0.0052 S22: -0.0435 S23: 0.2094 REMARK 3 S31: -0.5588 S32: -0.0514 S33: 0.0814 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 8DZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267589. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS SIRUS REMARK 200 BEAMLINE : MANACA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25100 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 71.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 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: 7MBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.7, 5% V/V DMSO, 8% W/V REMARK 280 PEG4000, 30% W/V PEG400, VAPOR DIFFUSION, 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 33.79500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.67600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.53300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.67600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.79500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.53300 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: 3400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET B 235 CA CB CG SD CE 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 A 540 O HOH A 541 1.80 REMARK 500 O HOH A 521 O HOH A 544 1.96 REMARK 500 O HOH A 545 O HOH A 548 2.00 REMARK 500 OG SER B 46 O HOH B 501 2.01 REMARK 500 OE1 GLU A 288 O HOH A 501 2.02 REMARK 500 O HOH A 536 O HOH A 542 2.04 REMARK 500 NE2 GLN A 189 F28 7YY A 403 2.04 REMARK 500 O HOH B 520 O HOH B 525 2.06 REMARK 500 O HOH A 547 O HOH A 550 2.09 REMARK 500 O HOH B 519 O HOH B 529 2.10 REMARK 500 O HOH A 506 O HOH A 547 2.11 REMARK 500 ND1 HIS B 41 F33 7YY B 402 2.15 REMARK 500 ND2 ASN A 180 O HOH A 502 2.16 REMARK 500 OD1 ASP B 263 O HOH B 502 2.17 REMARK 500 OD1 ASN B 221 O HOH B 502 2.19 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 NH2 ARG A 60 O LEU A 220 1455 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 60 CB - CG - CD ANGL. DEV. = -18.6 DEGREES REMARK 500 ARG A 60 CG - CD - NE ANGL. DEV. = -24.4 DEGREES REMARK 500 LEU A 220 CA - CB - CG ANGL. DEV. = 19.2 DEGREES 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 -129.28 55.80 REMARK 500 ASP A 48 38.04 -79.40 REMARK 500 ASN A 84 -120.67 50.54 REMARK 500 PRO A 184 36.42 -77.52 REMARK 500 LEU A 220 165.83 -37.96 REMARK 500 SER A 301 -177.80 -69.43 REMARK 500 ASP B 33 -127.12 56.32 REMARK 500 HIS B 41 0.09 -68.10 REMARK 500 SER B 46 1.07 -62.60 REMARK 500 ASN B 51 88.77 -162.21 REMARK 500 ASN B 84 -127.64 57.37 REMARK 500 TYR B 154 -108.15 59.80 REMARK 500 ASN B 221 -124.18 -103.70 REMARK 500 ARG B 222 -10.05 -151.42 REMARK 500 LEU B 262 -43.62 104.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 217 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8DZ1 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 8DZ1 B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 8DZ1 ILE A 49 UNP P0DTD1 MET 3312 ENGINEERED MUTATION SEQADV 8DZ1 ILE B 49 UNP P0DTD1 MET 3312 ENGINEERED MUTATION 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 ILE 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 ILE 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 DMS A 401 4 HET DMS A 402 4 HET 7YY A 403 37 HET DMS B 401 4 HET 7YY B 402 37 HETNAM DMS DIMETHYL SULFOXIDE HETNAM 7YY 6-[(6-CHLORANYL-2-METHYL-INDAZOL-5-YL)AMINO]-3-[(1- HETNAM 2 7YY METHYL-1,2,4-TRIAZOL-3-YL)METHYL]-1-[[2,4,5- HETNAM 3 7YY TRIS(FLUORANYL)PHENYL]METHYL]-1,3,5-TRIAZINE-2,4-DIONE FORMUL 3 DMS 3(C2 H6 O S) FORMUL 5 7YY 2(C22 H17 CL F3 N9 O2) FORMUL 8 HOH *82(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 GLY A 258 1 16 HELIX 8 AA8 ALA A 260 GLY A 275 1 16 HELIX 9 AA9 THR A 292 CYS A 300 1 9 HELIX 10 AB1 SER B 10 GLY B 15 1 6 HELIX 11 AB2 HIS B 41 CYS B 44 5 4 HELIX 12 AB3 GLU B 47 ASN B 51 5 5 HELIX 13 AB4 ASN B 53 LYS B 61 1 9 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 LEU B 262 GLY B 275 1 14 HELIX 20 AC2 THR B 292 CYS B 300 1 9 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 GLY A 29 N VAL A 18 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 GLY A 79 O LYS A 90 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N GLY A 149 O TYR A 161 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 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 VAL B 68 O LEU B 75 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 ILE B 78 O LYS B 90 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 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 CYS B 128 N PHE B 112 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 CRYST1 67.590 99.066 103.352 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 0.014795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009676 0.00000