HEADER VIRAL PROTEIN,HYDROLASE/INHIBITOR 11-JAN-21 7LCR TITLE IMPROVED FELINE DRUGS AS SARS-COV-2 MPRO INHIBITORS: STRUCTURE- TITLE 2 ACTIVITY STUDIES & MICELLAR SOLUBILIZATION FOR ENHANCED TITLE 3 BIOAVAILABILITY CAVEAT 7LCR GLU B 47 HAS WRONG CHIRALITY AT ATOM CA XTM B 401 HAS WRONG CAVEAT 2 7LCR CHIRALITY AT ATOM C04 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO; COMPND 5 EC: 3.4.22.69; COMPND 6 ENGINEERED: 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, COVID-19 VIRUS; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI O103:H2; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 585395; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: 12009 KEYWDS COVID-19, SARS-COV-2, 3CLPRO, CORONAVIRUS, MAIN PROTEASE, KINETICS, KEYWDS 2 SARS, VIRAL PROTEIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, KEYWDS 3 HYDROLASE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.B.KHAN,E.ARUTYUNOVA,H.S.YOUNG,M.J.LEMIEUX REVDAT 2 25-OCT-23 7LCR 1 REMARK REVDAT 1 07-DEC-22 7LCR 0 JRNL AUTH W.VUONG,C.FISCHER,M.B.KHAN,M.J.VAN BELKUM,T.LAMER, JRNL AUTH 2 K.D.WILLOUGHBY,J.LU,E.ARUTYUNOVA,M.A.JOYCE,H.A.SAFFRAN, JRNL AUTH 3 J.A.SHIELDS,H.S.YOUNG,J.A.NIEMAN,D.L.TYRRELL,M.J.LEMIEUX, JRNL AUTH 4 J.C.VEDERAS JRNL TITL IMPROVED SARS-COV-2 M PRO INHIBITORS BASED ON FELINE JRNL TITL 2 ANTIVIRAL DRUG GC376: STRUCTURAL ENHANCEMENTS, INCREASED JRNL TITL 3 SOLUBILITY, AND MICELLAR STUDIES. JRNL REF EUR.J.MED.CHEM. V. 222 13584 2021 JRNL REFN ISSN 0223-5234 JRNL PMID 34118724 JRNL DOI 10.1016/J.EJMECH.2021.113584 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 99833 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.490 REMARK 3 FREE R VALUE TEST SET COUNT : 3487 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 6.0500 - 4.8100 1.00 3169 167 0.1587 0.1941 REMARK 3 2 4.8100 - 4.2000 1.00 3138 165 0.1452 0.1920 REMARK 3 3 4.2000 - 3.8200 1.00 3174 158 0.1646 0.2102 REMARK 3 4 3.8200 - 3.5400 1.00 3163 166 0.1842 0.2465 REMARK 3 5 3.5400 - 3.3300 1.00 3177 168 0.2011 0.2390 REMARK 3 6 3.3300 - 3.1700 1.00 3182 168 0.2154 0.2751 REMARK 3 7 3.1700 - 3.0300 1.00 3139 164 0.2238 0.3094 REMARK 3 8 3.0300 - 2.9100 1.00 3169 165 0.2315 0.2599 REMARK 3 9 2.9100 - 2.8100 1.00 3124 163 0.2436 0.2896 REMARK 3 10 2.8100 - 2.7200 1.00 3198 167 0.2484 0.2732 REMARK 3 11 2.7200 - 2.6500 1.00 3162 166 0.2583 0.2978 REMARK 3 12 2.6500 - 2.5800 1.00 3147 168 0.2603 0.3212 REMARK 3 13 2.5800 - 2.5100 1.00 3180 164 0.2782 0.3283 REMARK 3 14 2.5100 - 2.4600 1.00 3134 167 0.2715 0.3247 REMARK 3 15 2.4600 - 2.4000 1.00 3210 171 0.2850 0.2901 REMARK 3 16 2.4000 - 2.3600 1.00 3127 165 0.2845 0.3002 REMARK 3 17 2.3600 - 2.3100 1.00 3190 164 0.2993 0.3456 REMARK 3 18 2.3100 - 2.2700 1.00 3157 169 0.3262 0.3091 REMARK 3 19 2.2700 - 2.2300 1.00 3154 167 0.3320 0.3531 REMARK 3 20 2.2300 - 2.2000 1.00 3143 164 0.3207 0.3746 REMARK 3 21 2.2000 - 2.1600 1.00 3143 163 0.3289 0.3870 REMARK 3 22 2.1600 - 2.1300 1.00 3167 161 0.3543 0.3599 REMARK 3 23 2.1300 - 2.1000 1.00 3121 165 0.3656 0.4076 REMARK 3 24 2.1000 - 2.0700 1.00 3213 172 0.3801 0.4146 REMARK 3 25 2.0700 - 2.0500 1.00 3135 169 0.4197 0.4702 REMARK 3 26 2.0500 - 2.0200 1.00 3145 165 0.4208 0.4006 REMARK 3 27 2.0200 - 2.0000 1.00 3150 162 0.4366 0.4664 REMARK 3 28 2.0000 - 1.9700 1.00 3250 170 0.4461 0.4524 REMARK 3 29 1.9700 - 1.9500 1.00 3139 161 0.4747 0.4679 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) : 0.446 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.882 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.00 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 : 0.017 4902 REMARK 3 ANGLE : 1.985 6660 REMARK 3 CHIRALITY : 0.117 748 REMARK 3 PLANARITY : 0.010 864 REMARK 3 DIHEDRAL : 18.663 676 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.8712 -2.8762 -16.0164 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.8996 REMARK 3 T33: 0.2905 T12: 0.0117 REMARK 3 T13: 0.0023 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 0.4439 L22: 0.3976 REMARK 3 L33: 1.3562 L12: -0.2160 REMARK 3 L13: -0.3088 L23: -0.0145 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.0205 S13: 0.0275 REMARK 3 S21: 0.0231 S22: -0.0287 S23: -0.0416 REMARK 3 S31: 0.0130 S32: 0.1414 S33: 0.0076 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "A" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "B" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LCR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253583. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-20 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99833 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 38.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.06 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 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: 6WTM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M HEPES PH 7.0, 20 % W/V PEG 6000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K 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 33.87000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.87000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.75500 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: 2940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 SG CYS A 145 H1 XTM A 401 1.36 REMARK 500 H SER A 62 OD1 ASN A 65 1.37 REMARK 500 OE1 GLU B 47 HB3 ASP B 48 1.52 REMARK 500 OG1 THR A 226 OD1 ASP A 229 1.85 REMARK 500 O HOH A 501 O HOH A 506 1.93 REMARK 500 OD1 ASN A 221 O HOH A 501 1.98 REMARK 500 N GLY B 79 O HOH B 501 2.02 REMARK 500 OG1 THR B 198 OE2 GLU B 240 2.03 REMARK 500 OD1 ASN A 277 O HOH A 502 2.10 REMARK 500 N SER A 62 OD1 ASN A 65 2.12 REMARK 500 O HOH B 547 O HOH B 576 2.12 REMARK 500 OG1 THR B 45 OE2 GLU B 47 2.16 REMARK 500 OE1 GLN A 69 OE1 GLN A 74 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 21 CB THR A 21 CG2 0.426 REMARK 500 GLU A 47 CB GLU A 47 CG 0.224 REMARK 500 GLU A 47 CG GLU A 47 CD -0.121 REMARK 500 GLU A 47 CD GLU A 47 OE2 0.145 REMARK 500 MET A 162 CB MET A 162 CG 0.666 REMARK 500 GLU A 240 CG GLU A 240 CD 0.096 REMARK 500 GLU A 240 CD GLU A 240 OE2 0.115 REMARK 500 GLU B 47 CB GLU B 47 CG 0.417 REMARK 500 GLU B 47 CG GLU B 47 CD 0.185 REMARK 500 GLU B 47 CD GLU B 47 OE1 -0.071 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 THR A 21 OG1 - CB - CG2 ANGL. DEV. = 22.0 DEGREES REMARK 500 GLU A 47 CB - CA - C ANGL. DEV. = -14.0 DEGREES REMARK 500 GLU A 47 OE1 - CD - OE2 ANGL. DEV. = -36.8 DEGREES REMARK 500 GLU A 47 CG - CD - OE1 ANGL. DEV. = 41.7 DEGREES REMARK 500 GLU A 47 CG - CD - OE2 ANGL. DEV. = -44.3 DEGREES REMARK 500 HIS A 64 N - CA - CB ANGL. DEV. = -13.9 DEGREES REMARK 500 ASN A 72 C - N - CA ANGL. DEV. = -22.9 DEGREES REMARK 500 ASN A 72 CB - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 ASN A 72 N - CA - CB ANGL. DEV. = 20.7 DEGREES REMARK 500 TYR A 161 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 MET A 162 CB - CG - SD ANGL. DEV. = -31.9 DEGREES REMARK 500 LYS A 236 CD - CE - NZ ANGL. DEV. = 15.7 DEGREES REMARK 500 GLU A 240 OE1 - CD - OE2 ANGL. DEV. = -28.4 DEGREES REMARK 500 GLU A 240 CG - CD - OE1 ANGL. DEV. = 37.3 DEGREES REMARK 500 GLU A 240 CG - CD - OE2 ANGL. DEV. = -32.4 DEGREES REMARK 500 ASP A 263 CB - CA - C ANGL. DEV. = 17.7 DEGREES REMARK 500 ASP A 263 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP A 263 CB - CG - OD2 ANGL. DEV. = -8.8 DEGREES REMARK 500 LEU A 271 CA - CB - CG ANGL. DEV. = -15.3 DEGREES REMARK 500 GLU B 47 N - CA - CB ANGL. DEV. = 34.5 DEGREES REMARK 500 GLU B 47 CB - CG - CD ANGL. DEV. = 19.5 DEGREES REMARK 500 GLU B 47 OE1 - CD - OE2 ANGL. DEV. = -11.5 DEGREES REMARK 500 GLU B 47 CG - CD - OE1 ANGL. DEV. = 13.5 DEGREES REMARK 500 GLU B 47 CA - C - O ANGL. DEV. = -15.2 DEGREES REMARK 500 GLU B 47 CA - C - N ANGL. DEV. = 22.8 DEGREES REMARK 500 ASP B 48 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 279 CB - CG - CD ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG B 279 CG - CD - NE ANGL. DEV. = 15.7 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 THR A 21 99.66 -169.97 REMARK 500 ASP A 33 -130.98 54.32 REMARK 500 CYS A 44 104.05 -47.85 REMARK 500 SER A 46 -117.05 -19.65 REMARK 500 MET A 49 63.51 20.04 REMARK 500 HIS A 64 0.15 -68.55 REMARK 500 ASN A 84 -123.74 57.15 REMARK 500 TYR A 154 -91.72 71.52 REMARK 500 GLN A 189 48.32 -83.81 REMARK 500 LYS A 269 -74.82 -48.95 REMARK 500 GLU A 270 -43.13 -19.65 REMARK 500 ASP B 33 -132.67 52.21 REMARK 500 GLU B 47 -100.20 29.52 REMARK 500 ASN B 84 -120.99 57.42 REMARK 500 TYR B 154 58.34 74.91 REMARK 500 ASP B 155 3.59 55.54 REMARK 500 PRO B 184 49.81 -85.87 REMARK 500 ASN B 238 41.66 70.30 REMARK 500 PHE B 305 71.96 -108.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 20 THR A 21 -135.64 REMARK 500 SER A 46 GLU A 47 122.42 REMARK 500 SER B 46 GLU B 47 100.63 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 HIS A 64 0.12 SIDE CHAIN REMARK 500 ASN A 72 0.09 SIDE CHAIN REMARK 500 GLU A 240 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 72 10.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XTM A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XTM B 401 DBREF 7LCR A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7LCR 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 XTM A 401 58 HET XTM B 401 58 HETNAM XTM N~2~-{[(3-FLUOROPHENYL)METHOXY]CARBONYL}-N-{(2S)-1- HETNAM 2 XTM HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3-YL]PROPAN-2-YL}-L- HETNAM 3 XTM LEUCINAMIDE FORMUL 3 XTM 2(C21 H30 F N3 O5) FORMUL 5 HOH *140(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 ILE A 43 5 3 HELIX 3 AA3 ASN A 53 LYS A 61 1 9 HELIX 4 AA4 SER A 62 PHE A 66 5 5 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 ASN A 274 1 15 HELIX 10 AB1 THR A 292 SER A 301 1 10 HELIX 11 AB2 SER B 10 GLY B 15 1 6 HELIX 12 AB3 HIS B 41 ILE B 43 5 3 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 MET B 235 1 10 HELIX 17 AB8 LYS B 236 ASN B 238 5 3 HELIX 18 AB9 THR B 243 LEU B 250 1 8 HELIX 19 AC1 LEU B 250 GLY B 258 1 9 HELIX 20 AC2 ALA B 260 GLY B 275 1 16 HELIX 21 AC3 THR B 292 CYS B 300 1 9 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69 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 SER A 81 O LYS A 88 SHEET 1 AA2 5 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 102 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 TYR A 126 N VAL A 114 SHEET 1 AA3 3 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 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 GLY B 79 O LYS B 90 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 VAL B 157 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ILE B 152 -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 TYR B 126 N VAL B 114 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 VAL B 157 GLU B 166 1 O VAL B 157 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C12 XTM A 401 1555 1555 2.04 LINK SG CYS B 145 C12 XTM B 401 1555 1555 2.11 SITE 1 AC1 11 PHE A 140 ASN A 142 GLY A 143 SER A 144 SITE 2 AC1 11 CYS A 145 HIS A 163 HIS A 164 MET A 165 SITE 3 AC1 11 GLU A 166 HIS A 172 GLN A 189 SITE 1 AC2 10 PHE B 140 ASN B 142 GLY B 143 SER B 144 SITE 2 AC2 10 CYS B 145 HIS B 163 HIS B 164 MET B 165 SITE 3 AC2 10 GLU B 166 GLN B 189 CRYST1 67.740 101.510 102.950 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 0.014762 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009851 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009713 0.00000 MTRIX1 1 -0.251812 -0.683933 0.684709 11.18332 1 MTRIX2 1 -0.679293 -0.379022 -0.628413 -12.27446 1 MTRIX3 1 0.689312 -0.623361 -0.369148 -24.79548 1