HEADER VIRAL PROTEIN,HYDROLASE/INHIBITOR 13-JAN-21 7LDL TITLE IMPROVED FELINE DRUGS AS SARS-COV-2 MPRO INHIBITORS: STRUCTURE- TITLE 2 ACTIVITY STUDIES & MICELLAR SOLUBILIZATION FOR ENHANCED TITLE 3 BIOAVAILABILITY 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,J.LU,E.ARUTYUNOVA,H.S.YOUNG,M.J.LEMIEUX REVDAT 2 18-OCT-23 7LDL 1 REMARK REVDAT 1 07-JUL-21 7LDL 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 46725 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2332 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 39.9200 - 5.1400 0.97 2700 143 0.2017 0.2305 REMARK 3 2 5.1400 - 4.0800 0.97 2679 141 0.1517 0.1934 REMARK 3 3 4.0800 - 3.5700 0.95 2619 138 0.1648 0.2118 REMARK 3 4 3.5600 - 3.2400 0.96 2719 142 0.1824 0.2617 REMARK 3 5 3.2400 - 3.0100 0.97 2668 141 0.1846 0.2502 REMARK 3 6 3.0100 - 2.8300 0.97 2693 142 0.1937 0.2720 REMARK 3 7 2.8300 - 2.6900 0.96 2661 140 0.2082 0.2939 REMARK 3 8 2.6900 - 2.5700 0.95 2629 139 0.2361 0.3081 REMARK 3 9 2.5700 - 2.4700 0.96 2672 140 0.2178 0.2457 REMARK 3 10 2.4700 - 2.3900 0.95 2643 139 0.2379 0.3127 REMARK 3 11 2.3900 - 2.3100 0.95 2617 138 0.2576 0.3234 REMARK 3 12 2.3100 - 2.2500 0.91 2522 132 0.2988 0.3737 REMARK 3 13 2.2500 - 2.1900 0.92 2585 137 0.3274 0.3583 REMARK 3 14 2.1900 - 2.1300 0.95 2657 140 0.3225 0.3566 REMARK 3 15 2.1300 - 2.0900 0.92 2531 128 0.3494 0.4401 REMARK 3 16 2.0900 - 2.0400 0.83 2292 120 0.4023 0.4311 REMARK 3 17 2.0400 - 2.0000 0.90 2506 132 0.3507 0.3667 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) : 0.366 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.89 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 4928 REMARK 3 ANGLE : 1.765 6705 REMARK 3 CHIRALITY : 0.087 752 REMARK 3 PLANARITY : 0.013 869 REMARK 3 DIHEDRAL : 20.936 682 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): 29.2073 1.9104 -17.2846 REMARK 3 T TENSOR REMARK 3 T11: 0.2589 T22: 0.2896 REMARK 3 T33: 0.3236 T12: 0.0250 REMARK 3 T13: 0.0110 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 1.7154 L22: 0.4318 REMARK 3 L33: 0.5460 L12: -0.2607 REMARK 3 L13: -0.2698 L23: 0.0054 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: 0.0402 S13: 0.0493 REMARK 3 S21: -0.0175 S22: -0.0052 S23: 0.0606 REMARK 3 S31: 0.0313 S32: 0.0453 S33: 0.0126 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" and (resid 1 through 5 or REMARK 3 resid 7 through 127 or resid 129 through REMARK 3 141 or resid 143 through 306)) 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" and (resid 1 through 5 or REMARK 3 resid 7 through 127 or resid 129 through REMARK 3 141 or resid 143 through 306)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7LDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253608. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-20 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 : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.52127 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 : 47333 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.540 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9900 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) : 2.07 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 (%): 56.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M HEPES PH REMARK 280 7.0, 20 % W/V PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24890 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 O GLU B 166 H311 XV4 B 401 1.54 REMARK 500 HH TYR A 126 O HOH A 501 1.55 REMARK 500 O HOH A 566 O HOH A 572 1.90 REMARK 500 O HOH A 514 O HOH A 568 1.95 REMARK 500 OH TYR A 126 O HOH A 501 1.97 REMARK 500 O HOH A 591 O HOH B 564 1.97 REMARK 500 OG SER B 123 O HOH B 501 2.02 REMARK 500 O HOH A 562 O HOH A 577 2.05 REMARK 500 O HOH B 595 O HOH B 611 2.05 REMARK 500 O HOH B 546 O HOH B 563 2.09 REMARK 500 O CYS A 300 O HOH A 502 2.09 REMARK 500 O HOH A 580 O HOH B 501 2.10 REMARK 500 O HOH B 590 O HOH B 613 2.11 REMARK 500 O HOH A 560 O HOH A 581 2.11 REMARK 500 O SER B 46 O HOH B 502 2.12 REMARK 500 O HOH B 586 O HOH B 588 2.13 REMARK 500 O HOH B 521 O HOH B 541 2.13 REMARK 500 O HOH A 606 O HOH A 607 2.13 REMARK 500 O HOH B 593 O HOH B 598 2.13 REMARK 500 O HOH A 558 O HOH A 594 2.13 REMARK 500 O HOH A 584 O HOH A 598 2.14 REMARK 500 OD2 ASP A 263 O HOH A 503 2.16 REMARK 500 O HOH A 601 O HOH A 605 2.17 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 589 O HOH B 546 1455 2.06 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 GLU A 55 CB GLU A 55 CG 0.321 REMARK 500 GLU A 55 CG GLU A 55 CD 0.144 REMARK 500 GLU A 55 CD GLU A 55 OE1 -0.090 REMARK 500 GLU A 55 CD GLU A 55 OE2 0.103 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 MET A 49 CB - CA - C ANGL. DEV. = 17.3 DEGREES REMARK 500 MET A 49 CG - SD - CE ANGL. DEV. = 19.6 DEGREES REMARK 500 GLU A 55 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 GLU A 55 OE1 - CD - OE2 ANGL. DEV. = -28.5 DEGREES REMARK 500 GLU A 55 CG - CD - OE1 ANGL. DEV. = 23.2 DEGREES REMARK 500 GLU A 55 CG - CD - OE2 ANGL. DEV. = -31.2 DEGREES REMARK 500 ILE A 59 CG1 - CB - CG2 ANGL. DEV. = 15.5 DEGREES REMARK 500 LYS A 90 CB - CG - CD ANGL. DEV. = 17.9 DEGREES REMARK 500 CYS A 128 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 LEU A 177 CA - CB - CG ANGL. DEV. = -14.3 DEGREES REMARK 500 ASP A 245 OD1 - CG - OD2 ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP A 245 CB - CG - OD1 ANGL. DEV. = 16.6 DEGREES REMARK 500 ASP A 245 CB - CG - OD2 ANGL. DEV. = -16.1 DEGREES REMARK 500 ILE A 249 CB - CA - C ANGL. DEV. = 15.7 DEGREES REMARK 500 ILE A 249 CA - CB - CG1 ANGL. DEV. = -24.1 DEGREES REMARK 500 ARG A 279 CG - CD - NE ANGL. DEV. = 14.2 DEGREES REMARK 500 LEU B 27 CB - CG - CD2 ANGL. DEV. = -10.8 DEGREES REMARK 500 CYS B 128 CA - CB - SG ANGL. DEV. = 7.6 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 -132.16 53.91 REMARK 500 HIS A 41 3.31 -65.65 REMARK 500 ASN A 51 72.29 -161.81 REMARK 500 ASN A 84 -122.87 52.09 REMARK 500 TYR A 154 -108.18 59.34 REMARK 500 PRO A 184 31.36 -89.24 REMARK 500 PHE A 305 -92.65 -130.43 REMARK 500 ASP B 33 -130.95 54.82 REMARK 500 HIS B 41 3.70 -65.32 REMARK 500 ASN B 51 74.71 -159.77 REMARK 500 ASN B 84 -120.91 52.24 REMARK 500 TYR B 154 -114.07 57.63 REMARK 500 PHE B 305 -90.94 -130.26 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 GLU A 55 0.17 SIDE CHAIN REMARK 500 ASP A 245 0.13 SIDE CHAIN REMARK 500 ASN A 274 0.10 SIDE CHAIN 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 607 DISTANCE = 6.07 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XV4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XV4 B 401 DBREF 7LDL A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7LDL 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 XV4 A 401 62 HET XV4 B 401 62 HETNAM XV4 N-[(2S)-1-({(2S)-1-HYDROXY-3-[(3S)-2-OXOPYRROLIDIN-3- HETNAM 2 XV4 YL]PROPAN-2-YL}AMINO)-4-METHYL-1-OXOPENTAN-2-YL]-4- HETNAM 3 XV4 METHOXY-1H-INDOLE-2-CARBOXAMIDE FORMUL 3 XV4 2(C23 H32 N4 O5) FORMUL 5 HOH *222(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 SER A 62 HIS A 64 5 3 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 CYS A 300 1 9 HELIX 12 AB3 SER B 10 GLY B 15 1 6 HELIX 13 AB4 HIS B 41 CYS B 44 5 4 HELIX 14 AB5 GLU B 47 ASN B 51 5 5 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 SER B 62 PHE B 66 5 5 HELIX 17 AB8 ILE B 200 ASN B 214 1 15 HELIX 18 AB9 THR B 226 TYR B 237 1 12 HELIX 19 AC1 THR B 243 LEU B 250 1 8 HELIX 20 AC2 LEU B 250 GLY B 258 1 9 HELIX 21 AC3 ALA B 260 GLY B 275 1 16 HELIX 22 AC4 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 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 89 N VAL A 36 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 LEU B 67 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 89 N VAL B 36 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N SER B 81 O LYS B 88 SHEET 1 AA5 5 TYR B 101 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O VAL B 157 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 TYR B 126 N VAL B 114 SHEET 1 AA6 3 TYR B 101 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 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 XV4 A 401 1555 1555 2.15 LINK SG CYS B 145 C12 XV4 B 401 1555 1555 2.14 SITE 1 AC1 15 HIS A 41 MET A 49 PHE A 140 ASN A 142 SITE 2 AC1 15 GLY A 143 SER A 144 CYS A 145 HIS A 163 SITE 3 AC1 15 HIS A 164 MET A 165 GLU A 166 HIS A 172 SITE 4 AC1 15 GLN A 189 THR A 190 ALA A 191 SITE 1 AC2 15 HIS B 41 PHE B 140 GLY B 143 SER B 144 SITE 2 AC2 15 CYS B 145 HIS B 163 HIS B 164 MET B 165 SITE 3 AC2 15 GLU B 166 HIS B 172 ASP B 187 GLN B 189 SITE 4 AC2 15 THR B 190 ALA B 191 HOH B 553 CRYST1 56.070 60.860 63.670 79.85 68.24 70.40 P 1 2 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 0.017835 -0.006350 -0.006755 0.00000 SCALE2 0.000000 0.017442 -0.001037 0.00000 SCALE3 0.000000 0.000000 0.016941 0.00000 MTRIX1 1 -0.996548 -0.059925 0.057455 59.44364 1 MTRIX2 1 -0.051647 -0.094333 -0.994200 -13.50435 1 MTRIX3 1 0.064998 -0.993735 0.090913 -15.73186 1