HEADER PEPTIDE BINDING PROTEIN 05-FEB-21 7NEV TITLE STRUCTURE OF THE HEMIACETAL COMPLEX BETWEEN THE SARS-COV-2 MAIN TITLE 2 PROTEASE AND LEUPEPTIN 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LEUPEPTIN; COMPND 10 CHAIN: B; COMPND 11 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; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: STREPTOMYCES ROSEUS; SOURCE 12 ORGANISM_TAXID: 66430 KEYWDS SARS-COV-2, MPRO, COVID-!9, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.GUENTHER,P.Y.A.REINKE,D.OBERTHUER,O.YEFANOV,L.GELISIO,H.M.GINN, AUTHOR 2 J.LIESKE,M.DOMARACKY,W.BREHM,A.RAHMANI MASHHOUR,T.A.WHITE,J.KNOSKA, AUTHOR 3 G.PENA ESPERANZA,F.KOUA,A.TOLSTIKOVA,M.GROESSLER,P.FISCHER, AUTHOR 4 V.HENNICKE,H.FLECKENSTEIN,F.TROST,M.GALCHENKOVA,Y.GEVORKOV,C.LI, AUTHOR 5 S.AWEL,P.L.XAVIER,N.ULLAH,H.ANDALEEB,S.FALKE,B.ALVES FRANCA, AUTHOR 6 M.SCHWINZER,H.BROGNARO,N.WERNER,M.PERBANDT,H.TIDOW,B.SEYCHELL, AUTHOR 7 T.BECK,S.MEIER,J.J.ZAITSEV-DOYLE,C.ROGERS,H.GIESELER,D.MELO, AUTHOR 8 D.C.F.MONTEIRO,I.DUNKEL,T.J.LANE,A.PECK,S.SAOUANE,J.HAKANPAEAE, AUTHOR 9 J.MEYER,H.NOEI,P.GRIBBON,B.ELLINGER,M.KUZIKOV,M.WOLF,L.ZHANG,C.EHRT, AUTHOR 10 J.PLETZER-ZELGERT,J.WOLLENHAUPT,C.FEILER,M.WEISS,F.SCHLUENZEN, AUTHOR 11 E.C.SCHULZ,P.MEHRABI,B.NORTON-BAKER,C.SCHMIDT,K.LORENZEN,R.SCHUBERT, AUTHOR 12 X.SUN,H.HAN,A.CHARI,Y.FERNANDEZ GARCIA,D.TURK,R.HILGENFELD,M.RAREY, AUTHOR 13 A.ZALIANI,H.N.CHAPMAN,A.PEARSON,C.BETZEL,A.MEENTS REVDAT 4 31-JAN-24 7NEV 1 JRNL REVDAT 3 19-MAY-21 7NEV 1 JRNL REVDAT 2 14-APR-21 7NEV 1 COMPND SOURCE JRNL REVDAT 1 03-MAR-21 7NEV 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.REINKE,D.OBERTHUER,O.YEFANOV,L.GELISIO,H.GINN, REMARK 1 AUTH 2 J.LIESKE,W.BREHM,A.RAHMANI MASHOUR,J.KNOSKA, REMARK 1 AUTH 3 G.PENA ESPERANZA,F.KOUA,A.TOLSTIKOVA,M.GROESSLER, REMARK 1 AUTH 4 H.FLECKENSTEIN,F.TROST,M.GALCHENKOVA,Y.GEVORKOV,C.LI,S.AWEL, REMARK 1 AUTH 5 L.X.PAULRAJ,N.ULLAH,S.FALKE,B.ALVES FRANCA,M.SCHWINZER, REMARK 1 AUTH 6 H.BROGNARO,N.WERNER,M.PERBANDT,B.SEYCHELL,S.MEIER,H.GISELER, REMARK 1 AUTH 7 D.MELO,I.DUNKEL,T.J.LANE,A.PECK,S.SAOUANE,J.HAKANPAEAE, REMARK 1 AUTH 8 J.MEYER,H.NOEI,P.GRIBBON,B.ELLINGER,M.KUZIKOV,M.WOLF, REMARK 1 AUTH 9 L.ZHANG,C.EHRT,J.PLETZER-ZELGERT,J.WOLLENHAUPT,C.FEILER, REMARK 1 AUTH10 M.WEISS,E.C.SCHULZ,P.MEHRABI,B.NORTON-BAKER,C.SCHMIDT, REMARK 1 AUTH11 K.LORENZEN,R.SCHUBERT,H.HAN,A.CHARI,Y.FERNANDEZ GARCIA, REMARK 1 AUTH12 R.HILGENFELD,M.RAREY,A.ZALIANI,H.N.CHAPMAN,A.PEARSON, REMARK 1 AUTH13 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. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 28743 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1439 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 23.8000 - 3.6600 0.99 2848 154 0.1419 0.1893 REMARK 3 2 3.6600 - 2.9100 0.99 2780 157 0.1595 0.1960 REMARK 3 3 2.9100 - 2.5400 0.98 2779 125 0.1870 0.2648 REMARK 3 4 2.5400 - 2.3100 0.98 2762 119 0.1918 0.2490 REMARK 3 5 2.3100 - 2.1400 0.97 2748 146 0.1938 0.2518 REMARK 3 6 2.1400 - 2.0200 0.98 2690 138 0.1934 0.2488 REMARK 3 7 2.0200 - 1.9100 0.97 2711 154 0.2176 0.2787 REMARK 3 8 1.9100 - 1.8300 0.96 2667 139 0.2406 0.2912 REMARK 3 9 1.8300 - 1.7600 0.96 2659 158 0.2605 0.2920 REMARK 3 10 1.7600 - 1.7000 0.96 2660 149 0.2960 0.3439 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) : 0.203 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.552 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.90 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 : 0.002 2478 REMARK 3 ANGLE : 0.561 3364 REMARK 3 CHIRALITY : 0.042 379 REMARK 3 PLANARITY : 0.006 436 REMARK 3 DIHEDRAL : 5.952 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4727 -10.4862 10.1831 REMARK 3 T TENSOR REMARK 3 T11: 0.0968 T22: 0.0786 REMARK 3 T33: 0.0505 T12: 0.0007 REMARK 3 T13: -0.0155 T23: 0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.0441 L22: 0.3632 REMARK 3 L33: 0.2181 L12: -0.1858 REMARK 3 L13: 0.2203 L23: -0.2352 REMARK 3 S TENSOR REMARK 3 S11: 0.0230 S12: -0.0483 S13: -0.0505 REMARK 3 S21: 0.0087 S22: -0.0113 S23: 0.0816 REMARK 3 S31: 0.0302 S32: -0.0069 S33: -0.0179 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 69 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0480 -11.5850 28.4663 REMARK 3 T TENSOR REMARK 3 T11: 0.2159 T22: 0.1800 REMARK 3 T33: 0.1378 T12: -0.0008 REMARK 3 T13: 0.0122 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 0.5443 L22: 0.9279 REMARK 3 L33: 0.1177 L12: -0.1264 REMARK 3 L13: -0.1627 L23: -0.1712 REMARK 3 S TENSOR REMARK 3 S11: -0.0133 S12: -0.1846 S13: 0.1946 REMARK 3 S21: 0.4114 S22: 0.1035 S23: 0.0406 REMARK 3 S31: -0.2716 S32: -0.0243 S33: 0.0645 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 70 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6306 -7.5434 9.5908 REMARK 3 T TENSOR REMARK 3 T11: 0.0545 T22: 0.0802 REMARK 3 T33: 0.0301 T12: 0.0037 REMARK 3 T13: 0.0003 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.2125 L22: 1.4757 REMARK 3 L33: 1.0984 L12: -0.2625 REMARK 3 L13: 0.2196 L23: -0.7917 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: 0.0313 S13: 0.0229 REMARK 3 S21: -0.1011 S22: -0.0560 S23: 0.0149 REMARK 3 S31: 0.0905 S32: 0.0374 S33: -0.0109 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7274 9.0655 5.1762 REMARK 3 T TENSOR REMARK 3 T11: 0.0792 T22: 0.1040 REMARK 3 T33: 0.1424 T12: -0.0261 REMARK 3 T13: -0.0087 T23: 0.0281 REMARK 3 L TENSOR REMARK 3 L11: 0.5428 L22: 0.6820 REMARK 3 L33: 2.2594 L12: -0.2066 REMARK 3 L13: 0.2585 L23: -0.6825 REMARK 3 S TENSOR REMARK 3 S11: -0.0359 S12: -0.0783 S13: 0.1197 REMARK 3 S21: 0.1369 S22: 0.0105 S23: -0.0942 REMARK 3 S31: -0.3117 S32: 0.0344 S33: -0.0447 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9976 17.8356 -11.4680 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.1573 REMARK 3 T33: 0.2749 T12: -0.0078 REMARK 3 T13: -0.0095 T23: 0.0713 REMARK 3 L TENSOR REMARK 3 L11: 0.4128 L22: 0.7290 REMARK 3 L33: 0.8735 L12: 0.0194 REMARK 3 L13: -0.4398 L23: -0.5138 REMARK 3 S TENSOR REMARK 3 S11: -0.0117 S12: 0.1052 S13: 0.2546 REMARK 3 S21: -0.0035 S22: -0.1326 S23: -0.1409 REMARK 3 S31: -0.1056 S32: 0.1906 S33: -0.0003 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.3576 20.0158 -7.3975 REMARK 3 T TENSOR REMARK 3 T11: 0.1636 T22: 0.1029 REMARK 3 T33: 0.2580 T12: 0.0132 REMARK 3 T13: 0.0456 T23: 0.0588 REMARK 3 L TENSOR REMARK 3 L11: 0.4606 L22: 0.0576 REMARK 3 L33: 0.2812 L12: 0.0438 REMARK 3 L13: 0.2885 L23: -0.0137 REMARK 3 S TENSOR REMARK 3 S11: 0.0657 S12: -0.0921 S13: 0.3706 REMARK 3 S21: 0.0777 S22: -0.0187 S23: 0.2314 REMARK 3 S31: -0.2170 S32: -0.0965 S33: -0.0380 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 293 THROUGH 303 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3787 0.4329 -10.4723 REMARK 3 T TENSOR REMARK 3 T11: 0.3353 T22: 0.1597 REMARK 3 T33: 0.2007 T12: -0.0299 REMARK 3 T13: 0.0187 T23: 0.0192 REMARK 3 L TENSOR REMARK 3 L11: 1.0218 L22: 0.3658 REMARK 3 L33: 0.1724 L12: 0.1864 REMARK 3 L13: -0.0629 L23: 0.2254 REMARK 3 S TENSOR REMARK 3 S11: -0.1338 S12: 0.2265 S13: -0.2240 REMARK 3 S21: -0.2580 S22: 0.0715 S23: 0.2322 REMARK 3 S31: 0.3269 S32: -0.0124 S33: -0.1315 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 7NEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-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 : 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS, DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29274 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 31.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6YNQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CO-CRYSTALLIZATION WITH THE COMPOUNDS REMARK 280 WAS ACHIEVED BY EQUILIBRATING A 6.25 MG/ML PROTEIN SOLUTION IN REMARK 280 20 MM HEPES BUFFER (PH 7.8) CONTAINING 1 MM DTT, 1 MMEDTA, AND REMARK 280 150 MM NACL AGAINST A RESERVOIR SOLUTION OF 100 MM MIB, PH 7.5, REMARK 280 CONTAINING 25% W/W 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 OBTAIN WELL-DIFFRACTING REMARK 280 CRYSTALS IN A REPRODUCIBLE WAY SEEDING WAS APPLIED FOR CRYSTAL REMARK 280 GROWTH. CRYSTALS APPEARED WITHIN A FEW HOURS AND REACHED THEIR REMARK 280 FINAL SIZE AFTER 2 - 3 DAYS. CRYSTALS WERE MANUALLY HARVESTED REMARK 280 AND FLASH-FROZEN IN LIQUID NITROGEN FOR SUBSEQUENT X-RAY REMARK 280 DIFFRACTION DATA COLLECTION., VAPOR DIFFUSION, 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 56.90550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.34100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.90550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.34100 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 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 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 810 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 862 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1014 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE LEUPEPTIN IS OLIGOPEPTIDE, A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: LEUPEPTIN REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 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 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 ARG A 217 NE CZ NH1 NH2 REMARK 470 MET A 235 SD CE REMARK 470 ARG A 298 CG CD NE CZ NH1 NH2 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 HOH A 660 O HOH A 863 2.17 REMARK 500 O HOH A 533 O HOH A 905 2.17 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 -134.04 53.56 REMARK 500 ASN A 51 76.88 -153.73 REMARK 500 ASN A 84 -116.72 53.83 REMARK 500 TYR A 154 -93.72 53.86 REMARK 500 ARG A 217 23.86 -145.80 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 A1057 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A1058 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1059 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A1060 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A1061 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A1062 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH A1063 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH A1064 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A1065 DISTANCE = 7.77 ANGSTROMS REMARK 525 HOH A1066 DISTANCE = 7.92 ANGSTROMS REMARK 525 HOH A1067 DISTANCE = 8.09 ANGSTROMS REMARK 525 HOH A1068 DISTANCE = 8.14 ANGSTROMS REMARK 525 HOH A1069 DISTANCE = 9.42 ANGSTROMS DBREF 7NEV A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 7NEV B 1 4 PDB 7NEV 7NEV 1 4 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 4 ACE LEU LEU AR7 HET ACE B 1 3 HET AR7 B 4 22 HET DMS A 401 4 HET DMS A 402 4 HET DMS A 403 4 HET IMD A 404 5 HET DMS A 405 4 HET CL A 406 1 HETNAM ACE ACETYL GROUP HETNAM AR7 AMINO{[(4S)-4-AMINO-5,5- HETNAM 2 AR7 DIHYDROXYPENTYL]AMINO}METHANIMINIUM HETNAM DMS DIMETHYL SULFOXIDE HETNAM IMD IMIDAZOLE HETNAM CL CHLORIDE ION FORMUL 2 ACE C2 H4 O FORMUL 2 AR7 C6 H17 N4 O2 1+ FORMUL 3 DMS 4(C2 H6 O S) FORMUL 6 IMD C3 H5 N2 1+ FORMUL 8 CL CL 1- FORMUL 9 HOH *577(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 PHE A 66 5 5 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 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N GLN A 19 O GLN A 69 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O THR A 25 N CYS A 22 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 3 TYR A 101 PHE A 103 0 SHEET 2 AA2 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA3 5 SER A 121 ALA A 129 0 SHEET 2 AA3 5 THR A 111 TYR A 118 -1 N ALA A 116 O SER A 123 SHEET 3 AA3 5 VAL A 148 ASP A 153 -1 O PHE A 150 N SER A 113 SHEET 4 AA3 5 CYS A 156 GLU A 166 -1 O SER A 158 N ASN A 151 SHEET 5 AA3 5 LEU B 2 LEU B 3 -1 O LEU B 2 N GLU A 166 LINK SG CYS A 145 C AAR7 B 4 1555 1555 1.69 LINK SG CYS A 145 C BAR7 B 4 1555 1555 1.72 LINK C ACE B 1 N LEU B 2 1555 1555 1.33 LINK C LEU B 3 N AAR7 B 4 1555 1555 1.33 LINK C LEU B 3 N BAR7 B 4 1555 1555 1.33 CRYST1 113.811 52.682 46.230 90.00 102.78 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 0.008786 0.000000 0.001994 0.00000 SCALE2 0.000000 0.018982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022181 0.00000