HEADER HYDROLASE 22-SEP-20 7AGA TITLE STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO AT7519 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 5, COMPND 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, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SARS-COV-2, MPRO, COVID-19, PEPTIDE BINDING PROTEIN, VIRUS PROTEASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.GUENTHER,P.REINKE,D.OBERTHUER,O.YEFANOV,L.GELISIO,H.GINN,J.LIESKE, AUTHOR 2 M.DOMARACKY,W.BREHM,A.RAHMANI MASHOUR,T.A.WHITE,J.KNOSKA,G.PENA AUTHOR 3 ESPERANZA,F.KOUA,A.TOLSTIKOVA,M.GROESSLER,P.FISCHER,V.HENNICKE, AUTHOR 4 H.FLECKENSTEIN,F.TROST,M.GALCHENKOVA,Y.GEVORKOV,C.LI,S.AWEL, AUTHOR 5 L.X.PAULRAJ,N.ULLAH,H.ANDALEEB,N.WERNER,S.FALKE,W.HINRICHS,B.ALVES AUTHOR 6 FRANCA,M.SCHWINZER,H.BROGNARO,M.PERBANDT,H.TIDOW,B.SEYCHELL,T.BECK, AUTHOR 7 S.MEIER,J.J.DOYLE,H.GISELER,D.MELO,I.DUNKEL,T.J.LANE,A.PECK, AUTHOR 8 S.SAOUANE,J.HAKANPAEAE,J.MEYER,H.NOEI,J.BOGER,P.GRIBBON,B.ELLINGER, AUTHOR 9 M.KUZIKOV,M.WOLF,L.ZHANG,C.EHRT,J.PLETZER-ZELGERT,J.WOLLENHAUPT, AUTHOR 10 C.FEILER,M.WEISS,E.C.SCHULZ,P.MEHRABI,B.NORTON-BAKER,C.SCHMIDT, AUTHOR 11 K.LORENZEN,R.SCHUBERT,H.HAN,A.CHARI,Y.FERNANDEZ GARCIA,D.TURK, AUTHOR 12 R.HILGENFELD,M.RAREY,A.ZALIANI,H.N.CHAPMAN,A.PEARSON,C.BETZEL, AUTHOR 13 A.MEENTS REVDAT 6 31-JAN-24 7AGA 1 JRNL REVDAT 5 24-AUG-22 7AGA 1 REMARK REVDAT 4 19-MAY-21 7AGA 1 JRNL REVDAT 3 14-APR-21 7AGA 1 COMPND SOURCE JRNL REMARK REVDAT 3 2 1 SITE ATOM REVDAT 2 09-DEC-20 7AGA 1 JRNL REVDAT 1 02-DEC-20 7AGA 0 JRNL AUTH S.GUNTHER,P.Y.A.REINKE,Y.FERNANDEZ-GARCIA,J.LIESKE,T.J.LANE, JRNL AUTH 2 H.M.GINN,F.H.M.KOUA,C.EHRT,W.EWERT,D.OBERTHUER,O.YEFANOV, JRNL AUTH 3 S.MEIER,K.LORENZEN,B.KRICHEL,J.D.KOPICKI,L.GELISIO,W.BREHM, JRNL AUTH 4 I.DUNKEL,B.SEYCHELL,H.GIESELER,B.NORTON-BAKER, JRNL AUTH 5 B.ESCUDERO-PEREZ,M.DOMARACKY,S.SAOUANE,A.TOLSTIKOVA, JRNL AUTH 6 T.A.WHITE,A.HANLE,M.GROESSLER,H.FLECKENSTEIN,F.TROST, JRNL AUTH 7 M.GALCHENKOVA,Y.GEVORKOV,C.LI,S.AWEL,A.PECK,M.BARTHELMESS, JRNL AUTH 8 F.SCHLUNZEN,P.LOURDU XAVIER,N.WERNER,H.ANDALEEB,N.ULLAH, JRNL AUTH 9 S.FALKE,V.SRINIVASAN,B.A.FRANCA,M.SCHWINZER,H.BROGNARO, JRNL AUTH10 C.ROGERS,D.MELO,J.J.ZAITSEVA-DOYLE,J.KNOSKA, JRNL AUTH11 G.E.PENA-MURILLO,A.R.MASHHOUR,V.HENNICKE,P.FISCHER, JRNL AUTH12 J.HAKANPAA,J.MEYER,P.GRIBBON,B.ELLINGER,M.KUZIKOV,M.WOLF, JRNL AUTH13 A.R.BECCARI,G.BOURENKOV,D.VON STETTEN,G.POMPIDOR,I.BENTO, JRNL AUTH14 S.PANNEERSELVAM,I.KARPICS,T.R.SCHNEIDER,M.M.GARCIA-ALAI, JRNL AUTH15 S.NIEBLING,C.GUNTHER,C.SCHMIDT,R.SCHUBERT,H.HAN,J.BOGER, JRNL AUTH16 D.C.F.MONTEIRO,L.ZHANG,X.SUN,J.PLETZER-ZELGERT, JRNL AUTH17 J.WOLLENHAUPT,C.G.FEILER,M.S.WEISS,E.C.SCHULZ,P.MEHRABI, JRNL AUTH18 K.KARNICAR,A.USENIK,J.LOBODA,H.TIDOW,A.CHARI,R.HILGENFELD, JRNL AUTH19 C.UETRECHT,R.COX,A.ZALIANI,T.BECK,M.RAREY,S.GUNTHER,D.TURK, JRNL AUTH20 W.HINRICHS,H.N.CHAPMAN,A.R.PEARSON,C.BETZEL,A.MEENTS JRNL TITL X-RAY SCREENING IDENTIFIES ACTIVE SITE AND ALLOSTERIC JRNL TITL 2 INHIBITORS OF SARS-COV-2 MAIN PROTEASE. JRNL REF SCIENCE V. 372 642 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33811162 JRNL DOI 10.1126/SCIENCE.ABF7945 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.GUENTHER,P.Y.A.,REINKE,Y.,FERNANDEZ-GARCIA,J.,LIESKE,T.J., REMARK 1 AUTH 2 LANE,H.M.,GINN,F.H.M.,KOUA,C.,EHRT,W.,EWERT,D.,OBERTHUER,O., REMARK 1 AUTH 3 YEFANOV,S.,MEIER,K.,LORENZEN,B.,KRICHEL,J.D.,KOPICKI,L., REMARK 1 AUTH 4 GELISIO,W.,BREHM,I.,DUNKEL,B.,SEYCHELL,H.,GIESELER,B., REMARK 1 AUTH 5 NORTON-BAKER,B.,ESCUDERO-PEREZ,M.,DOMARACKY,S.,SAOUANE,A., REMARK 1 AUTH 6 TOLSTIKOVA,T.A.,WHITE,A.,HANLE,M.,GROESSLER,H.,FLECKENSTEIN, REMARK 1 AUTH 7 F.,TROST,M.,GALCHENKOVA,Y.,GEVORKOV,C.,LI,S.,AWEL,A.PECK,M., REMARK 1 AUTH 8 BARTHELMESS,F.,SCHLUENZEN,L.X.,PAULRAJ,N.,WERNER,H., REMARK 1 AUTH 9 ANDALEEB,N.,ULLAH,S.,FALKE,V.,SRINIVASAN,B.,FRANCA,M., REMARK 1 AUTH10 SCHWINZER,H.,BROGNARO,C.,ROGERS,D.,MELO,J.J.,DOYLE,J., REMARK 1 AUTH11 KNOSKA,G.E.,PENA MURILLO,A.,RAHMANI MASHHOUR,F.,GUICKING,V., REMARK 1 AUTH12 HENNICKE,P.,FISCHER,J.,HAKANPAEAE,J.,MEYER,P.,GRIBBON,B., REMARK 1 AUTH13 ELLINGER,M.,KUZIKOV,M.,WOLF,G.,BURENKOV,D.,VON STETTEN,G., REMARK 1 AUTH14 POMPIDOR,I.,BENTO,S.,PANNEERSELVAM,I.,KARPICS,T.R., REMARK 1 AUTH15 SCHNEIDER,M.,GARCIA ALAI,S.,NIEBLING,C.,GUENTHER,C.,SCHMIDT, REMARK 1 AUTH16 R.,SCHUBERT,H.,HAN,J.,BOGER,D.,MONTEIRO,L.,ZHANG,X.,SUN,J., REMARK 1 AUTH17 PLETZER-ZELGERT,J.,WOLLENHAUPT,C.,FEILER,M.,WEISS,E.C., REMARK 1 AUTH18 SCHULZ,P.,MEHRABI,K.,KARNICAR,A.,USENIK,J.,LOBODA,H.,TIDOW, REMARK 1 AUTH19 A.,CHARI,R.,HILGENFELD,C.,UETRECHT,R.,COX,A.,ZALIANI,T., REMARK 1 AUTH20 BECK,M.,RAREY,S.,GUENTHER,D.,TURK,W.,HINRICHS,H.N.,CHAPMAN, REMARK 1 AUTH21 A.,PEARSON,C.,BETZEL,A.MEENTS REMARK 1 TITL INHIBITION OF SARS-COV-2 MAIN PROTEASE BY ALLOSTERIC REMARK 1 TITL 2 DRUG-BINDING REMARK 1 REF BIORXIV 2020 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2020.11.12.378422 REMARK 2 REMARK 2 RESOLUTION. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13-2998_9999 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 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 28529 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1426 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 30.9300 - 3.6200 0.94 2677 140 0.1477 0.1628 REMARK 3 2 3.6200 - 2.8700 0.88 2451 130 0.1551 0.2119 REMARK 3 3 2.8700 - 2.5100 1.00 2774 146 0.1764 0.2386 REMARK 3 4 2.5100 - 2.2800 1.00 2753 144 0.1795 0.2085 REMARK 3 5 2.2800 - 2.1200 1.00 2746 145 0.1935 0.2298 REMARK 3 6 2.1200 - 1.9900 1.00 2746 145 0.2208 0.2766 REMARK 3 7 1.9900 - 1.8900 0.99 2730 143 0.2688 0.2980 REMARK 3 8 1.8900 - 1.8100 1.00 2741 144 0.3031 0.3475 REMARK 3 9 1.8100 - 1.7400 1.00 2745 145 0.3429 0.3700 REMARK 3 10 1.7400 - 1.6800 1.00 2740 144 0.3810 0.4273 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) : 0.311 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.455 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.97 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 2613 REMARK 3 ANGLE : 0.761 3562 REMARK 3 CHIRALITY : 0.049 393 REMARK 3 PLANARITY : 0.006 464 REMARK 3 DIHEDRAL : 10.831 1553 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.6864 -10.6143 9.9204 REMARK 3 T TENSOR REMARK 3 T11: 0.2067 T22: 0.2013 REMARK 3 T33: 0.2386 T12: 0.0003 REMARK 3 T13: 0.0063 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 1.6582 L22: 1.3198 REMARK 3 L33: 0.5214 L12: 0.2709 REMARK 3 L13: -0.0380 L23: 0.2249 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: -0.0329 S13: -0.0638 REMARK 3 S21: -0.0277 S22: -0.0274 S23: 0.0941 REMARK 3 S31: 0.1290 S32: 0.0372 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.8603 -14.2272 17.4834 REMARK 3 T TENSOR REMARK 3 T11: 0.2449 T22: 0.2691 REMARK 3 T33: 0.2574 T12: 0.0155 REMARK 3 T13: 0.0283 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 1.6322 L22: 2.4553 REMARK 3 L33: 1.2465 L12: 0.1618 REMARK 3 L13: 1.2420 L23: -0.5015 REMARK 3 S TENSOR REMARK 3 S11: 0.0957 S12: -0.1677 S13: -0.2103 REMARK 3 S21: 0.2738 S22: -0.0555 S23: -0.2148 REMARK 3 S31: 0.1690 S32: -0.0362 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 214 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.4856 0.7949 6.8568 REMARK 3 T TENSOR REMARK 3 T11: 0.2052 T22: 0.2036 REMARK 3 T33: 0.2216 T12: -0.0032 REMARK 3 T13: 0.0083 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.5982 L22: 1.5733 REMARK 3 L33: 1.5849 L12: -0.3125 REMARK 3 L13: 0.4445 L23: -1.5156 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: 0.0028 S13: 0.0061 REMARK 3 S21: 0.0199 S22: -0.0075 S23: -0.0833 REMARK 3 S31: -0.0649 S32: 0.0711 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 215 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6927 16.1930 -9.7312 REMARK 3 T TENSOR REMARK 3 T11: 0.2331 T22: 0.2324 REMARK 3 T33: 0.2102 T12: -0.0181 REMARK 3 T13: -0.0125 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 3.1610 L22: 1.5283 REMARK 3 L33: 2.7094 L12: -0.0291 REMARK 3 L13: -0.4994 L23: -0.2853 REMARK 3 S TENSOR REMARK 3 S11: 0.0164 S12: 0.0899 S13: 0.1681 REMARK 3 S21: -0.0256 S22: 0.0015 S23: 0.0153 REMARK 3 S31: -0.1734 S32: -0.1652 S33: -0.0009 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 7AGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292111313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28529 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 30.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.620 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: 6YB7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CO-CRYSTALLIZATION WITH THE COMPOUND REMARK 280 WAS ACHIEVED BY EQULIBRATING A 6.25 MG/ML PROTEIN SOLUTION IN 20 REMARK 280 MM HEPES BUFFER (PH 7.8) CONTAINING 1 MM DTT, 1MM EDTA, AND 150 REMARK 280 MM NACL AGAINST A RESERVOIR SOLUTION OF 100 MM MIB BUFFER (2:3:3 REMARK 280 MOLAR RATIO OF MALONIC ACID, IMIDAZOLE, AND BORIC ACID), PH 7.5, REMARK 280 CONTAINING 25% V/V PEG 1500 AND 5% V/V DMSO. PRIOR TO REMARK 280 CRYSTALLIZATION COMPOUND SOLUTIONS IN DMSO WERE DRIED ONTO THE REMARK 280 WELLS OF SWISSCI 96-WELL PLATES. TO ACHIEVE REPRODUCIBLE CRYSTAL REMARK 280 GROWTH SEEDING WAS USED. CRYSTALS APPEARED WITHIN A FEW HOURS REMARK 280 AND REACHED THEIR FINAL SIZE AFTER 2 -3 DAYS. CRYSTALS WERE REMARK 280 MANUALLY HARVESTED AND FLASH COOLED IN LIQUID NITROGEN FOR REMARK 280 SUBSEQUENT X-RAY DIFFRACTION DATA COLLECTION., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 291K 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 56.18600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.32050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.18600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.32050 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: 6400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 CL CL A 402 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: 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 -134.75 55.74 REMARK 500 ASN A 51 74.61 -162.46 REMARK 500 ASN A 84 -118.55 54.13 REMARK 500 TYR A 154 163.89 80.81 REMARK 500 TYR A 154 -76.77 61.27 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 729 DISTANCE = 6.22 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LZE A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 DMS A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 411 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7A1U RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO FUSIDIC ACID REMARK 900 RELATED ID: 6YT8 RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO PYRITHIONE ZINC REMARK 900 RELATED ID: 6YNQ RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO 2-METHYL-1-TETRALONE. REMARK 900 RELATED ID: 6YVF RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO AZD6482. REMARK 900 RELATED ID: 6YZ6 RELATED DB: PDB REMARK 900 STRUCTURE OF THE HEMIACETAL COMPLEX BETWEEN THE SARS-COV-2 MAIN REMARK 900 PROTEASE AND LEUPEPTIN REMARK 900 RELATED ID: 7AF0 RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO IPIDACRINE. REMARK 900 RELATED ID: 7ABU RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO RS102895 REMARK 900 RELATED ID: 7ADW RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO TOLPERISONE DBREF 7AGA 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 LZE A 401 42 HET CL A 402 1 HET CL A 403 1 HET DMS A 404 10 HET DMS A 405 10 HET DMS A 406 10 HET DMS A 407 10 HET DMS A 408 10 HET DMS A 409 10 HET DMS A 410 10 HET DMS A 411 10 HETNAM LZE 4-{[(2,6-DICHLOROPHENYL)CARBONYL]AMINO}-N-PIPERIDIN-4- HETNAM 2 LZE YL-1H-PYRAZOLE-3-CARBOXAMIDE HETNAM CL CHLORIDE ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 LZE C16 H17 CL2 N5 O2 FORMUL 3 CL 2(CL 1-) FORMUL 5 DMS 8(C2 H6 O S) FORMUL 13 HOH *229(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 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 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 TYR A 101 PHE A 103 0 SHEET 2 AA2 5 VAL A 157 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASN A 151 -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 TYR A 101 PHE A 103 0 SHEET 2 AA3 3 VAL A 157 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SITE 1 AC1 14 GLU A 47 LEU A 50 PRO A 108 GLY A 109 SITE 2 AC1 14 GLN A 110 ASP A 153 VAL A 202 ASN A 203 SITE 3 AC1 14 ILE A 249 PRO A 293 PHE A 294 ARG A 298 SITE 4 AC1 14 HOH A 607 HOH A 687 SITE 1 AC2 1 ALA A 285 SITE 1 AC3 4 PRO A 52 ASN A 53 TYR A 54 GLU A 55 SITE 1 AC4 6 MET A 6 PHE A 8 SER A 123 GLN A 127 SITE 2 AC4 6 ARG A 298 HOH A 627 SITE 1 AC5 8 GLN A 74 LEU A 75 ARG A 76 PHE A 223 SITE 2 AC5 8 THR A 224 ASP A 263 HOH A 532 HOH A 549 SITE 1 AC6 5 PHE A 140 LEU A 141 ASN A 142 HIS A 163 SITE 2 AC6 5 GLU A 166 SITE 1 AC7 6 PRO A 96 LYS A 97 THR A 98 LEU A 272 SITE 2 AC7 6 ASN A 274 GLY A 275 SITE 1 AC8 7 ASP A 56 ILE A 59 PRO A 132 THR A 196 SITE 2 AC8 7 THR A 198 GLU A 240 HOH A 553 SITE 1 AC9 2 LEU A 287 HOH A 542 SITE 1 AD1 3 GLY A 15 MET A 17 LYS A 97 CRYST1 112.372 52.641 44.585 90.00 102.67 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 0.008899 0.000000 0.002001 0.00000 SCALE2 0.000000 0.018997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022989 0.00000