HEADER HYDROLASE 09-OCT-20 7AMJ TITLE STRUCTURE OF SARS-COV-2 MAIN PROTEASE BOUND TO PD 168568. 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 5 31-JAN-24 7AMJ 1 JRNL REVDAT 4 19-MAY-21 7AMJ 1 JRNL REVDAT 3 14-APR-21 7AMJ 1 COMPND SOURCE JRNL REMARK REVDAT 2 09-DEC-20 7AMJ 1 JRNL REVDAT 1 02-DEC-20 7AMJ 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. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.440 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34582 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1675 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.3257 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3621 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2358 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.34 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.211 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 43 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2072 -10.1721 9.4827 REMARK 3 T TENSOR REMARK 3 T11: 0.0786 T22: 0.0797 REMARK 3 T33: 0.1081 T12: -0.0005 REMARK 3 T13: 0.0124 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.6977 L22: 1.7069 REMARK 3 L33: 0.7866 L12: -0.0086 REMARK 3 L13: 0.5516 L23: -0.3984 REMARK 3 S TENSOR REMARK 3 S11: -0.0177 S12: 0.0204 S13: -0.0494 REMARK 3 S21: -0.0873 S22: -0.0242 S23: 0.0837 REMARK 3 S31: 0.0523 S32: 0.0652 S33: 0.0226 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 44 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): 13.9842 -16.3836 20.2012 REMARK 3 T TENSOR REMARK 3 T11: 0.1217 T22: 0.1522 REMARK 3 T33: 0.1986 T12: 0.0105 REMARK 3 T13: 0.0101 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.5365 L22: 2.3903 REMARK 3 L33: 2.1102 L12: 0.7834 REMARK 3 L13: 0.7745 L23: -0.4988 REMARK 3 S TENSOR REMARK 3 S11: 0.0878 S12: -0.2467 S13: -0.1012 REMARK 3 S21: 0.2004 S22: -0.1616 S23: -0.1085 REMARK 3 S31: 0.0102 S32: -0.1762 S33: 0.1006 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 A 180 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1656 -2.3904 7.6874 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.0900 REMARK 3 T33: 0.0900 T12: 0.0052 REMARK 3 T13: -0.0059 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 3.0138 L22: 3.0770 REMARK 3 L33: 1.6254 L12: 0.3486 REMARK 3 L13: 0.6387 L23: -0.5081 REMARK 3 S TENSOR REMARK 3 S11: -0.1059 S12: 0.0274 S13: 0.1148 REMARK 3 S21: -0.1966 S22: 0.0458 S23: 0.0831 REMARK 3 S31: -0.1354 S32: 0.0220 S33: 0.0450 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 181 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3899 8.8473 5.0859 REMARK 3 T TENSOR REMARK 3 T11: 0.1500 T22: 0.1316 REMARK 3 T33: 0.1480 T12: -0.0311 REMARK 3 T13: -0.0099 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.7472 L22: 1.8864 REMARK 3 L33: 3.6712 L12: -0.8669 REMARK 3 L13: 1.0253 L23: -2.5524 REMARK 3 S TENSOR REMARK 3 S11: -0.2157 S12: -0.0130 S13: 0.0567 REMARK 3 S21: 0.3102 S22: 0.0120 S23: -0.1645 REMARK 3 S31: -0.4663 S32: -0.0652 S33: 0.1402 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 215 A 305 REMARK 3 ORIGIN FOR THE GROUP (A): 12.6068 15.6803 -9.9506 REMARK 3 T TENSOR REMARK 3 T11: 0.1259 T22: 0.1545 REMARK 3 T33: 0.0947 T12: -0.0347 REMARK 3 T13: -0.0123 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 2.7809 L22: 1.9785 REMARK 3 L33: 2.1265 L12: -0.0063 REMARK 3 L13: -0.3117 L23: -0.3651 REMARK 3 S TENSOR REMARK 3 S11: 0.0157 S12: 0.1214 S13: 0.1031 REMARK 3 S21: -0.0329 S22: 0.0254 S23: 0.0623 REMARK 3 S31: 0.0185 S32: -0.2123 S33: -0.0465 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7AMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111720. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-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) : 1.0332 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 : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34590 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 54.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.66800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 6YNQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 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 56.34100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.46400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.34100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.46400 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 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 APPLY THE FOLLOWING TO CHAINS: A 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 401 LIES ON A SPECIAL POSITION. REMARK 375 N11 RMZ A 409 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 -134.25 53.99 REMARK 500 ASN A 51 66.00 -151.56 REMARK 500 ASN A 84 -121.45 55.48 REMARK 500 TYR A 154 -88.11 51.21 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 831 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH A 832 DISTANCE = 6.94 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL 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 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 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RMZ A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YNQ RELATED DB: PDB REMARK 900 RELATED ID: 6YT8 RELATED DB: PDB REMARK 900 RELATED ID: 6YZ6 RELATED DB: PDB REMARK 900 RELATED ID: 7A1U RELATED DB: PDB REMARK 900 RELATED ID: 6YVF RELATED DB: PDB REMARK 900 RELATED ID: 7ABU RELATED DB: PDB REMARK 900 RELATED ID: 7ADW RELATED DB: PDB REMARK 900 RELATED ID: 7AGA RELATED DB: PDB REMARK 900 RELATED ID: 7AF0 RELATED DB: PDB REMARK 900 RELATED ID: 7AHA RELATED DB: PDB REMARK 900 RELATED ID: 7AKU RELATED DB: PDB DBREF 7AMJ 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 CL A 401 1 HET DMS A 402 10 HET DMS A 403 10 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 RMZ A 409 53 HETNAM CL CHLORIDE ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM RMZ (3~{S})-3-[2-[4-(3,4-DIMETHYLPHENYL)PIPERAZIN-1- HETNAM 2 RMZ YL]ETHYL]-2,3-DIHYDROISOINDOL-1-ONE HETSYN RMZ 3-(2-(4-(3,4-DIMETHYLPHENYL)PIPERAZIN-1-YL)ETHYL) HETSYN 2 RMZ ISOINDOLIN-1-ONE FORMUL 2 CL CL 1- FORMUL 3 DMS 7(C2 H6 O S) FORMUL 10 RMZ C22 H27 N3 O FORMUL 11 HOH *332(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 VAL A 68 O LEU A 75 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 GLY A 29 N VAL A 18 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 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 ALA A 173 N MET A 165 SITE 1 AC1 3 SER A 284 ALA A 285 HOH A 565 SITE 1 AC2 6 MET A 6 PHE A 8 SER A 123 GLN A 127 SITE 2 AC2 6 ARG A 298 HOH A 694 SITE 1 AC3 8 GLN A 74 LEU A 75 ARG A 76 PHE A 223 SITE 2 AC3 8 THR A 224 ASP A 263 HOH A 553 HOH A 558 SITE 1 AC4 4 GLY A 15 MET A 17 LYS A 97 HOH A 537 SITE 1 AC5 6 PHE A 140 LEU A 141 ASN A 142 HIS A 163 SITE 2 AC5 6 MET A 165 GLU A 166 SITE 1 AC6 3 HIS A 64 ASN A 65 PHE A 223 SITE 1 AC7 3 TYR A 101 PHE A 103 HOH A 692 SITE 1 AC8 6 PRO A 96 LYS A 97 GLN A 273 ASN A 274 SITE 2 AC8 6 GLY A 275 HOH A 506 SITE 1 AC9 8 ASN A 142 ILE A 213 LEU A 253 GLN A 256 SITE 2 AC9 8 CYS A 300 SER A 301 HOH A 658 HOH A 689 CRYST1 112.682 52.928 44.714 90.00 102.89 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 0.008875 0.000000 0.002030 0.00000 SCALE2 0.000000 0.018894 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022942 0.00000