HEADER VIRAL PROTEIN 25-JUN-24 9CDK TITLE SARS-COV-2 MPRO A173V MUTANT IN COMPLEX WITH SMALL MOLECULE INHIBITOR TITLE 2 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 ENGINEERED: YES; COMPND 7 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; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, MPRO, 3CL, MAIN PROTEASE, INHIBITOR, SMALL MOLECULE, KEYWDS 2 MPRO61, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TANG,J.R.KENNESON,K.S.ANDERSON REVDAT 2 12-MAR-25 9CDK 1 JRNL REVDAT 1 05-FEB-25 9CDK 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. 1.61 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34328 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1660 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 31.0300 - 3.6800 1.00 2811 120 0.1552 0.1821 REMARK 3 2 3.6800 - 2.9200 1.00 2750 141 0.1668 0.2210 REMARK 3 3 2.9200 - 2.5500 1.00 2717 143 0.1846 0.2193 REMARK 3 4 2.5500 - 2.3200 1.00 2700 155 0.1841 0.2321 REMARK 3 5 2.3200 - 2.1500 1.00 2733 145 0.1786 0.2115 REMARK 3 6 2.1500 - 2.0300 1.00 2672 160 0.1901 0.2303 REMARK 3 7 2.0300 - 1.9300 1.00 2704 138 0.1965 0.2361 REMARK 3 8 1.9300 - 1.8400 1.00 2718 141 0.2220 0.2657 REMARK 3 9 1.8400 - 1.7700 1.00 2719 129 0.2359 0.2745 REMARK 3 10 1.7700 - 1.7100 1.00 2704 128 0.2555 0.2901 REMARK 3 11 1.7100 - 1.6600 1.00 2690 131 0.2887 0.3551 REMARK 3 12 1.6600 - 1.6100 1.00 2750 129 0.3147 0.3195 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.580 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 : 0.900 NULL REMARK 3 CHIRALITY : 0.055 378 REMARK 3 PLANARITY : 0.008 445 REMARK 3 DIHEDRAL : 11.852 353 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6779 -10.6020 9.9200 REMARK 3 T TENSOR REMARK 3 T11: 0.1673 T22: 0.1527 REMARK 3 T33: 0.1776 T12: 0.0060 REMARK 3 T13: 0.0078 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 1.4125 L22: 1.0144 REMARK 3 L33: 1.0700 L12: 0.0693 REMARK 3 L13: 0.0709 L23: -0.6135 REMARK 3 S TENSOR REMARK 3 S11: -0.0665 S12: -0.0104 S13: -0.0383 REMARK 3 S21: -0.0843 S22: 0.0311 S23: 0.0240 REMARK 3 S31: 0.1474 S32: -0.0041 S33: 0.0495 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1317 -12.7740 27.5334 REMARK 3 T TENSOR REMARK 3 T11: 0.3142 T22: 0.3384 REMARK 3 T33: 0.2537 T12: -0.0044 REMARK 3 T13: 0.0174 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.9934 L22: 2.1689 REMARK 3 L33: 1.4813 L12: 1.2937 REMARK 3 L13: 0.4815 L23: -0.2912 REMARK 3 S TENSOR REMARK 3 S11: 0.1627 S12: -0.3642 S13: 0.2450 REMARK 3 S21: 0.3407 S22: -0.2347 S23: -0.0157 REMARK 3 S31: -0.1765 S32: -0.2612 S33: 0.0965 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.7628 -14.1889 10.6191 REMARK 3 T TENSOR REMARK 3 T11: 0.2045 T22: 0.2028 REMARK 3 T33: 0.1860 T12: 0.0279 REMARK 3 T13: 0.0293 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.5593 L22: 2.0592 REMARK 3 L33: 0.6793 L12: -0.0260 REMARK 3 L13: 0.4304 L23: -0.7330 REMARK 3 S TENSOR REMARK 3 S11: -0.0394 S12: 0.0110 S13: -0.0928 REMARK 3 S21: -0.2661 S22: -0.0033 S23: -0.1118 REMARK 3 S31: 0.1368 S32: 0.0140 S33: 0.0249 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4041 2.3191 7.8942 REMARK 3 T TENSOR REMARK 3 T11: 0.1836 T22: 0.1831 REMARK 3 T33: 0.1874 T12: -0.0065 REMARK 3 T13: -0.0045 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 0.4604 L22: 1.0916 REMARK 3 L33: 1.1661 L12: -0.0374 REMARK 3 L13: 0.0677 L23: -1.1287 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: -0.0365 S13: -0.0195 REMARK 3 S21: -0.0087 S22: -0.0150 S23: 0.0014 REMARK 3 S31: 0.0375 S32: -0.0176 S33: 0.0442 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 236 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9230 22.9148 -10.9533 REMARK 3 T TENSOR REMARK 3 T11: 0.2585 T22: 0.2537 REMARK 3 T33: 0.2421 T12: -0.0238 REMARK 3 T13: 0.0074 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 2.3163 L22: 1.4414 REMARK 3 L33: 1.5849 L12: 0.5895 REMARK 3 L13: -0.3926 L23: -0.0655 REMARK 3 S TENSOR REMARK 3 S11: 0.0045 S12: 0.0046 S13: 0.0892 REMARK 3 S21: -0.1264 S22: 0.0415 S23: -0.2105 REMARK 3 S31: -0.2186 S32: 0.0399 S33: 0.0004 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 237 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9203 13.8725 -9.2856 REMARK 3 T TENSOR REMARK 3 T11: 0.1540 T22: 0.1970 REMARK 3 T33: 0.1553 T12: -0.0256 REMARK 3 T13: 0.0025 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 1.9177 L22: 1.1392 REMARK 3 L33: 2.6267 L12: 0.0207 REMARK 3 L13: -0.0489 L23: 0.3129 REMARK 3 S TENSOR REMARK 3 S11: 0.0600 S12: 0.0587 S13: -0.0496 REMARK 3 S21: -0.0071 S22: -0.0024 S23: 0.0061 REMARK 3 S31: 0.0555 S32: -0.0689 S33: -0.0532 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 9CDK 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_1000285268. 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 : 7.0 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) : 0.92010 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 : 34342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 31.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.92800 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 (%): 37.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1% W/V TRYPTONE, 0.001 M SODIUM AZIDE, REMARK 280 0.05 M HEPES SODIUM PH 7.0, 20% W/V POLYETHYLENE GLYCOL 3,350, REMARK 280 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 57.44350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.77900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.44350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.77900 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 679 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 767 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 770 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 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 LYS A 100 CD CE NZ REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 217 NE CZ NH1 NH2 REMARK 470 ARG A 298 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 A 738 O HOH A 771 2.00 REMARK 500 O HOH A 766 O HOH A 774 2.03 REMARK 500 O HOH A 667 O HOH A 710 2.09 REMARK 500 O HOH A 544 O HOH A 712 2.10 REMARK 500 OD1 ASN A 51 O HOH A 501 2.14 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 521 O HOH A 531 2554 1.92 REMARK 500 O HOH A 622 O HOH A 733 4556 2.01 REMARK 500 O HOH A 572 O HOH A 611 4556 2.10 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 -131.81 53.80 REMARK 500 ASN A 51 62.86 -159.89 REMARK 500 ASN A 84 -123.48 51.76 REMARK 500 MET A 130 109.42 -56.82 REMARK 500 TYR A 154 -107.72 58.63 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 776 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A 777 DISTANCE = 6.39 ANGSTROMS DBREF 9CDK A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 SEQADV 9CDK VAL A 173 UNP P0DTD1 ALA 3436 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 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 VAL 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 401 116 HET DMS A 402 10 HET DMS A 403 10 HET DMS A 404 10 HET DMS A 405 20 HET CL A 406 1 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 HETNAM DMS DIMETHYL SULFOXIDE HETNAM CL CHLORIDE ION FORMUL 2 XEK C28 H19 CL2 F N4 O4 FORMUL 3 DMS 4(C2 H6 O S) FORMUL 7 CL CL 1- FORMUL 8 HOH *277(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 GLU A 47 ASN A 51 5 5 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 GLY A 215 1 16 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 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 89 N VAL A 36 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N ILE A 78 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 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 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O VAL A 173 N MET A 165 CRYST1 114.887 53.558 44.551 90.00 103.15 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 0.008704 0.000000 0.002034 0.00000 SCALE2 0.000000 0.018671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023051 0.00000