HEADER VIRAL PROTEIN 25-JUN-24 9CDL TITLE SARS-COV-2 MPRO E166V/L50F DOUBLE MUTANT IN COMPLEX WITH SMALL TITLE 2 MOLECULE INHIBITOR MPRO61 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE NSP5; COMPND 3 CHAIN: A; 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; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, MAIN PROTEASE, MPRO, 3CL, DRUG RESISTANT MUTANT, E166V, KEYWDS 2 L50F, ANTIVIRAL, INHIBITOR, MPRO61, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TANG,J.R.KENNESON,K.HUYNH,K.S.ANDERSON REVDAT 2 12-MAR-25 9CDL 1 JRNL REVDAT 1 05-FEB-25 9CDL 0 JRNL AUTH J.R.KENNESON,C.PAPINI,S.TANG,K.HUYNH,C.H.ZHANG, JRNL AUTH 2 W.L.JORGENSEN,K.S.ANDERSON JRNL TITL EXPLORING POSSIBLE DRUG-RESISTANT VARIANTS OF SARS-COV-2 JRNL TITL 2 MAIN PROTEASE (M PRO ) WITH NONCOVALENT PRECLINICAL JRNL TITL 3 CANDIDATE, MPRO61. JRNL REF ACS BIO MED CHEM AU V. 5 215 2025 JRNL REFN ESSN 2694-2437 JRNL PMID 39990941 JRNL DOI 10.1021/ACSBIOMEDCHEMAU.4C00109 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 2071 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 31.7000 - 3.7500 1.00 2724 142 0.1486 0.1738 REMARK 3 2 3.7500 - 2.9800 1.00 2669 149 0.1655 0.1710 REMARK 3 3 2.9800 - 2.6000 1.00 2647 154 0.1879 0.1954 REMARK 3 4 2.6000 - 2.3600 1.00 2651 133 0.1899 0.2384 REMARK 3 5 2.3600 - 2.1900 1.00 2662 135 0.1815 0.2258 REMARK 3 6 2.1900 - 2.0600 1.00 2631 142 0.1791 0.2188 REMARK 3 7 2.0600 - 1.9600 1.00 2636 151 0.1867 0.2385 REMARK 3 8 1.9600 - 1.8800 1.00 2643 110 0.1981 0.2384 REMARK 3 9 1.8800 - 1.8000 1.00 2664 140 0.2102 0.2281 REMARK 3 10 1.8000 - 1.7400 1.00 2664 120 0.2235 0.2663 REMARK 3 11 1.7400 - 1.6900 1.00 2626 130 0.2317 0.2543 REMARK 3 12 1.6900 - 1.6400 1.00 2636 126 0.2486 0.2906 REMARK 3 13 1.6400 - 1.5900 1.00 2611 160 0.2830 0.3050 REMARK 3 14 1.5900 - 1.5600 1.00 2589 156 0.2954 0.3133 REMARK 3 15 1.5600 - 1.5200 0.98 2616 123 0.3046 0.2836 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.830 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 NULL REMARK 3 ANGLE : 0.774 NULL REMARK 3 CHIRALITY : 0.050 377 REMARK 3 PLANARITY : 0.009 446 REMARK 3 DIHEDRAL : 13.516 892 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8435 -10.3972 9.2281 REMARK 3 T TENSOR REMARK 3 T11: 0.1521 T22: 0.1475 REMARK 3 T33: 0.2215 T12: -0.0150 REMARK 3 T13: -0.0143 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 2.0648 L22: 1.7937 REMARK 3 L33: 1.0292 L12: -0.6265 REMARK 3 L13: 0.7554 L23: -0.7613 REMARK 3 S TENSOR REMARK 3 S11: 0.1753 S12: -0.1287 S13: -0.3580 REMARK 3 S21: -0.1449 S22: 0.1132 S23: 0.3283 REMARK 3 S31: 0.1963 S32: -0.1598 S33: -0.2243 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7535 -7.0714 29.1021 REMARK 3 T TENSOR REMARK 3 T11: 0.3784 T22: 0.3106 REMARK 3 T33: 0.1964 T12: 0.0894 REMARK 3 T13: 0.0217 T23: 0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.4263 L22: 6.4898 REMARK 3 L33: 1.2175 L12: -1.4308 REMARK 3 L13: -0.6806 L23: 2.7444 REMARK 3 S TENSOR REMARK 3 S11: -0.1000 S12: -0.4265 S13: 0.1452 REMARK 3 S21: 1.1804 S22: 0.1897 S23: -0.0123 REMARK 3 S31: -0.0191 S32: -0.4339 S33: 0.0409 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 91 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.8789 -19.7281 19.4985 REMARK 3 T TENSOR REMARK 3 T11: 0.2573 T22: 0.2663 REMARK 3 T33: 0.3448 T12: -0.0429 REMARK 3 T13: -0.0195 T23: 0.1210 REMARK 3 L TENSOR REMARK 3 L11: 1.1741 L22: 2.0195 REMARK 3 L33: 1.4408 L12: -0.4847 REMARK 3 L13: 0.1780 L23: 0.0774 REMARK 3 S TENSOR REMARK 3 S11: 0.0846 S12: -0.2975 S13: -0.2925 REMARK 3 S21: 0.2609 S22: 0.1683 S23: 0.4791 REMARK 3 S31: 0.3781 S32: -0.3749 S33: -0.1383 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 92 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.2148 -4.3415 6.8242 REMARK 3 T TENSOR REMARK 3 T11: 0.1272 T22: 0.1101 REMARK 3 T33: 0.1088 T12: -0.0040 REMARK 3 T13: 0.0030 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.0048 L22: 2.5779 REMARK 3 L33: 1.5558 L12: -0.2259 REMARK 3 L13: 0.9408 L23: -0.9620 REMARK 3 S TENSOR REMARK 3 S11: 0.0394 S12: -0.0338 S13: -0.1095 REMARK 3 S21: -0.2073 S22: 0.0597 S23: 0.1705 REMARK 3 S31: 0.1428 S32: -0.0777 S33: -0.0599 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.2997 9.1762 4.7730 REMARK 3 T TENSOR REMARK 3 T11: 0.1412 T22: 0.1167 REMARK 3 T33: 0.1313 T12: -0.0204 REMARK 3 T13: 0.0069 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 1.1255 L22: 1.5507 REMARK 3 L33: 1.1984 L12: -0.3058 REMARK 3 L13: -0.0638 L23: -0.8126 REMARK 3 S TENSOR REMARK 3 S11: -0.1484 S12: 0.1289 S13: 0.1464 REMARK 3 S21: 0.2826 S22: -0.0234 S23: -0.1541 REMARK 3 S31: -0.3807 S32: 0.0782 S33: 0.1276 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 250 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7961 19.7314 -10.0284 REMARK 3 T TENSOR REMARK 3 T11: 0.2210 T22: 0.2602 REMARK 3 T33: 0.2460 T12: 0.0081 REMARK 3 T13: 0.0176 T23: 0.0828 REMARK 3 L TENSOR REMARK 3 L11: 1.7322 L22: 1.6090 REMARK 3 L33: 1.0511 L12: -0.3253 REMARK 3 L13: -0.8493 L23: 0.7929 REMARK 3 S TENSOR REMARK 3 S11: 0.0784 S12: 0.3983 S13: 0.4615 REMARK 3 S21: -0.1544 S22: 0.0722 S23: -0.2171 REMARK 3 S31: -0.2022 S32: -0.0330 S33: -0.1085 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 251 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.8637 13.6045 -10.3126 REMARK 3 T TENSOR REMARK 3 T11: 0.1816 T22: 0.2998 REMARK 3 T33: 0.1741 T12: -0.0208 REMARK 3 T13: 0.0018 T23: 0.0638 REMARK 3 L TENSOR REMARK 3 L11: 3.0630 L22: 0.9582 REMARK 3 L33: 2.9245 L12: -0.4050 REMARK 3 L13: -0.2275 L23: 0.6298 REMARK 3 S TENSOR REMARK 3 S11: 0.0532 S12: 0.4157 S13: 0.1312 REMARK 3 S21: -0.0338 S22: -0.0309 S23: 0.0144 REMARK 3 S31: 0.0300 S32: -0.3761 S33: -0.0298 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 9CDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000285273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.920 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 34.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.16200 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) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 1.68800 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 (%): 39.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0-6.5, 10% 2-PROPANOL, REMARK 280 15-20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.84450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.27250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.84450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.27250 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 690 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 694 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 718 LIES ON A SPECIAL POSITION. 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 A 306 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 503 O HOH A 590 2.10 REMARK 500 O HOH A 503 O HOH A 684 2.13 REMARK 500 O HOH A 752 O HOH A 754 2.16 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 531 O HOH A 639 2555 2.15 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 -133.01 54.83 REMARK 500 ASN A 84 -123.65 52.33 REMARK 500 TYR A 154 -99.37 61.08 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 755 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 756 DISTANCE = 6.25 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9CDK RELATED DB: PDB REMARK 900 DIFFERENT MUTANT BINDS TO THE SAME INHIBITOR DBREF 9CDL A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 9CDL PHE A 50 UNP P0DTD1 LEU 3313 ENGINEERED MUTATION SEQADV 9CDL VAL A 166 UNP P0DTD1 GLU 3429 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 MET PHE 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 VAL 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 HET XEK A 401 58 HETNAM XEK (5P)-5-[(1P,3M,3'P)-3-{3-CHLORO-5-[(2-CHLOROPHENYL) HETNAM 2 XEK METHOXY]-4-FLUOROPHENYL}-2-OXO-2H-[1,3'-BIPYRIDIN]-5- HETNAM 3 XEK YL]-1-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE FORMUL 2 XEK C28 H19 CL2 F N4 O4 FORMUL 3 HOH *256(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 PHE A 50 5 6 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 LYS A 61 HIS A 64 5 4 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 TYR A 237 1 12 HELIX 8 AA8 THR A 243 LEU A 250 1 8 HELIX 9 AA9 LEU A 250 GLY A 258 1 9 HELIX 10 AB1 ALA A 260 GLY A 275 1 16 HELIX 11 AB2 THR A 292 GLY A 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 VAL A 35 N LEU A 32 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 VAL A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA2 5 VAL A 148 ASP A 153 -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 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 VAL 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 CRYST1 115.689 54.545 44.433 90.00 101.24 90.00 C 1 2 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 0.008644 0.000000 0.001718 0.00000 SCALE2 0.000000 0.018333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022946 0.00000