HEADER HYDROLASE 21-DEC-20 7L5D TITLE THE CRYSTAL STRUCTURE OF SARS-COV-2 MAIN PROTEASE IN COMPLEX WITH TITLE 2 DEMETHYLATED ANALOG OF MASITINIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 3CL-PRO, 3CLP, MAIN PROTEASE, MPRO, NON-STRUCTURAL PROTEIN COMPND 5 5, NSP5, SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PMCSG53 KEYWDS SARS-COV-2, COVID-19, 3CL, MAIN PROTEASE, MASITINIB, DEMETHYLATION, KEYWDS 2 ANALOG, STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF KEYWDS 3 INFECTIOUS DISEASES, CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TAN,N.I.MALTSEVA,R.P.JEDRZEJCZAK,A.JOACHIMIAK,CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 5 18-OCT-23 7L5D 1 REMARK REVDAT 4 01-SEP-21 7L5D 1 JRNL REVDAT 3 25-AUG-21 7L5D 1 JRNL REVDAT 2 28-JUL-21 7L5D 1 JRNL REVDAT 1 30-DEC-20 7L5D 0 JRNL AUTH N.DRAYMAN,J.K.DEMARCO,K.A.JONES,S.A.AZIZI,H.M.FROGGATT, JRNL AUTH 2 K.TAN,N.I.MALTSEVA,S.CHEN,V.NICOLAESCU,S.DVORKIN,K.FURLONG, JRNL AUTH 3 R.S.KATHAYAT,M.R.FIRPO,V.MASTRODOMENICO,E.A.BRUCE, JRNL AUTH 4 M.M.SCHMIDT,R.JEDRZEJCZAK,M.A.MUNOZ-ALIA,B.SCHUSTER,V.NAIR, JRNL AUTH 5 K.Y.HAN,A.O'BRIEN,A.TOMATSIDOU,B.MEYER,M.VIGNUZZI, JRNL AUTH 6 D.MISSIAKAS,J.W.BOTTEN,C.B.BROOKE,H.LEE,S.C.BAKER, JRNL AUTH 7 B.C.MOUNCE,N.S.HEATON,W.E.SEVERSON,K.E.PALMER,B.C.DICKINSON, JRNL AUTH 8 A.JOACHIMIAK,G.RANDALL,S.TAY JRNL TITL MASITINIB IS A BROAD CORONAVIRUS 3CL INHIBITOR THAT BLOCKS JRNL TITL 2 REPLICATION OF SARS-COV-2. JRNL REF SCIENCE V. 373 931 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 34285133 JRNL DOI 10.1126/SCIENCE.ABG5827 REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 49625 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2444 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 44.3600 - 4.0600 1.00 2861 151 0.1516 0.1694 REMARK 3 2 4.0600 - 3.2200 1.00 2793 164 0.1584 0.1604 REMARK 3 3 3.2200 - 2.8200 1.00 2840 148 0.1769 0.2142 REMARK 3 4 2.8200 - 2.5600 1.00 2787 147 0.1893 0.2327 REMARK 3 5 2.5600 - 2.3800 1.00 2811 146 0.1826 0.2263 REMARK 3 6 2.3800 - 2.2400 1.00 2787 143 0.1744 0.2011 REMARK 3 7 2.2400 - 2.1200 1.00 2812 131 0.1682 0.2015 REMARK 3 8 2.1200 - 2.0300 1.00 2811 140 0.1661 0.2214 REMARK 3 9 2.0300 - 1.9500 1.00 2829 131 0.1790 0.1975 REMARK 3 10 1.9500 - 1.8900 1.00 2751 162 0.1860 0.2169 REMARK 3 11 1.8900 - 1.8300 1.00 2794 142 0.1851 0.2161 REMARK 3 12 1.8300 - 1.7700 1.00 2804 123 0.1927 0.1989 REMARK 3 13 1.7700 - 1.7300 1.00 2795 142 0.2179 0.2394 REMARK 3 14 1.7300 - 1.6900 1.00 2815 140 0.2327 0.2639 REMARK 3 15 1.6900 - 1.6500 1.00 2771 159 0.2650 0.3265 REMARK 3 16 1.6500 - 1.6100 0.98 2709 148 0.2977 0.2944 REMARK 3 17 1.6100 - 1.5800 0.87 2411 127 0.3167 0.3233 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) : 0.188 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.688 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.28 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 : 0.009 2531 REMARK 3 ANGLE : 1.030 3442 REMARK 3 CHIRALITY : 0.063 378 REMARK 3 PLANARITY : 0.007 447 REMARK 3 DIHEDRAL : 21.582 921 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2780 11.8454 19.1668 REMARK 3 T TENSOR REMARK 3 T11: 0.1795 T22: 0.1962 REMARK 3 T33: 0.2250 T12: -0.0460 REMARK 3 T13: 0.0062 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 0.6462 L22: 1.2731 REMARK 3 L33: 2.1412 L12: 0.2050 REMARK 3 L13: -0.1084 L23: 0.5252 REMARK 3 S TENSOR REMARK 3 S11: 0.1164 S12: -0.1274 S13: 0.0363 REMARK 3 S21: 0.1061 S22: 0.0463 S23: -0.2638 REMARK 3 S31: -0.1913 S32: 0.3827 S33: -0.1641 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0860 7.3653 14.7609 REMARK 3 T TENSOR REMARK 3 T11: 0.1579 T22: 0.1584 REMARK 3 T33: 0.1773 T12: -0.0243 REMARK 3 T13: 0.0043 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.7964 L22: 1.5735 REMARK 3 L33: 1.8741 L12: 0.0226 REMARK 3 L13: -0.4400 L23: 0.1262 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: -0.0280 S13: 0.0720 REMARK 3 S21: -0.0189 S22: 0.0378 S23: -0.0727 REMARK 3 S31: -0.2013 S32: 0.0657 S33: -0.0659 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 301 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0979 -15.2925 5.7023 REMARK 3 T TENSOR REMARK 3 T11: 0.2182 T22: 0.2242 REMARK 3 T33: 0.2261 T12: -0.0566 REMARK 3 T13: 0.0080 T23: -0.0193 REMARK 3 L TENSOR REMARK 3 L11: 0.9643 L22: 1.3090 REMARK 3 L33: 2.7105 L12: 0.6315 REMARK 3 L13: 0.7319 L23: 0.9994 REMARK 3 S TENSOR REMARK 3 S11: 0.0168 S12: 0.0125 S13: -0.1065 REMARK 3 S21: 0.0567 S22: -0.0407 S23: 0.0116 REMARK 3 S31: 0.3847 S32: -0.2705 S33: 0.0232 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 7L5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97919 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49652 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 44.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.84500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 7JU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M MES, 20% (W/V) REMARK 280 PEG6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 48.71800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.64800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.71800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.64800 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: 6220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 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 535 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 630 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 636 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 688 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 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 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 GLU A 47 CG CD OE1 OE2 REMARK 470 MET A 49 SD CE REMARK 470 LEU A 50 CG CD1 CD2 REMARK 470 ASN A 51 CG OD1 ND2 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 LYS A 5 95.09 -68.06 REMARK 500 ASP A 33 -133.93 51.82 REMARK 500 GLU A 47 35.40 -86.51 REMARK 500 LEU A 50 -75.81 -62.74 REMARK 500 ASN A 84 -122.90 56.05 REMARK 500 TYR A 154 -112.28 54.37 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 XNJ A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 DBREF 7L5D A 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 HET XNJ A 401 35 HET DMS A 402 8 HET DMS A 403 4 HET DMS A 404 4 HET DMS A 405 8 HET GOL A 406 12 HET GOL A 407 6 HET GOL A 408 6 HET GOL A 409 6 HETNAM XNJ N-(4-METHYL-3-{[4-(PYRIDIN-3-YL)-1,3-THIAZOL-2- HETNAM 2 XNJ YL]AMINO}PHENYL)-4-[(PIPERAZIN-1-YL)METHYL]BENZAMIDE HETNAM DMS DIMETHYL SULFOXIDE HETNAM GOL GLYCEROL HETSYN XNJ DEMETHYLATED MASITINIB HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 XNJ C27 H28 N6 O S FORMUL 3 DMS 4(C2 H6 O S) FORMUL 7 GOL 4(C3 H8 O3) FORMUL 11 HOH *191(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 MET A 49 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 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 87 N CYS A 38 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 THR A 175 N MET A 162 SITE 1 AC1 16 THR A 24 THR A 25 HIS A 41 CYS A 44 SITE 2 AC1 16 SER A 46 MET A 49 PHE A 140 LEU A 141 SITE 3 AC1 16 ASN A 142 SER A 144 CYS A 145 HIS A 163 SITE 4 AC1 16 HIS A 164 MET A 165 GLU A 166 HOH A 574 SITE 1 AC2 4 ARG A 40 ASN A 84 CYS A 85 GOL A 406 SITE 1 AC3 4 TYR A 37 TYR A 101 PHE A 103 GOL A 408 SITE 1 AC4 7 MET A 6 ALA A 7 PHE A 8 SER A 123 SITE 2 AC4 7 GLN A 127 ARG A 298 HOH A 507 SITE 1 AC5 5 GLY A 15 MET A 17 TRP A 31 ALA A 70 SITE 2 AC5 5 GLY A 71 SITE 1 AC6 10 ARG A 40 PRO A 52 ASN A 53 TYR A 54 SITE 2 AC6 10 GLU A 55 ARG A 188 DMS A 402 HOH A 510 SITE 3 AC6 10 HOH A 583 HOH A 616 SITE 1 AC7 6 GLU A 166 ARG A 188 GLN A 189 THR A 190 SITE 2 AC7 6 GLN A 192 HOH A 550 SITE 1 AC8 4 LYS A 100 TYR A 101 DMS A 403 HOH A 605 SITE 1 AC9 4 LEU A 57 ARG A 60 LYS A 61 HOH A 502 CRYST1 97.436 81.296 51.558 90.00 114.41 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 0.010263 0.000000 0.004659 0.00000 SCALE2 0.000000 0.012301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021300 0.00000