HEADER PEPTIDE BINDING PROTEIN 06-MAY-20 6YZ6 OBSLTE 10-MAR-21 6YZ6 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: MAIN PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN; COMPND 5 EC: 3.4.19.12,3.4.22.-,3.4.22.69,2.7.7.48,3.6.4.12,3.6.4.13,3.1.13.-, COMPND 6 3.1.-.-,2.1.1.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LEUPEPTIN; COMPND 10 CHAIN: C; 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; 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 3 14-APR-21 6YZ6 1 JRNL REVDAT 2 10-MAR-21 6YZ6 1 OBSLTE REVDAT 1 20-MAY-20 6YZ6 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.SCHLUENZEN,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 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33811162 JRNL DOI 10.1126/SCIENCE.ABF7945 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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 (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 28745 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.216 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 0.1459 0.1802 REMARK 3 2 3.6600 - 2.9100 0.99 2780 157 0.1561 0.1686 REMARK 3 3 2.9100 - 2.5400 0.98 2779 125 0.1752 0.2452 REMARK 3 4 2.5400 - 2.3100 0.98 2762 119 0.1763 0.2214 REMARK 3 5 2.3100 - 2.1400 0.97 2749 146 0.1832 0.2190 REMARK 3 6 2.1400 - 2.0200 0.98 2690 138 0.1830 0.2448 REMARK 3 7 2.0200 - 1.9100 0.97 2712 154 0.2070 0.2720 REMARK 3 8 1.9100 - 1.8300 0.96 2667 139 0.2346 0.2964 REMARK 3 9 1.8300 - 1.7600 0.96 2659 158 0.2504 0.2656 REMARK 3 10 1.7600 - 1.7000 0.96 2660 149 0.2886 0.3319 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) : 0.178 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.063 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.68 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 : 0.005 2561 REMARK 3 ANGLE : 0.738 3482 REMARK 3 CHIRALITY : 0.048 384 REMARK 3 PLANARITY : 0.005 456 REMARK 3 DIHEDRAL : 25.213 355 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): 7.4706 -10.4744 10.1804 REMARK 3 T TENSOR REMARK 3 T11: 0.1559 T22: 0.1271 REMARK 3 T33: 0.1021 T12: 0.0011 REMARK 3 T13: -0.0115 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 1.1727 L22: 0.7397 REMARK 3 L33: 0.7189 L12: -0.5865 REMARK 3 L13: 0.5112 L23: -0.8161 REMARK 3 S TENSOR REMARK 3 S11: 0.0308 S12: -0.0527 S13: -0.0601 REMARK 3 S21: 0.0013 S22: 0.0166 S23: 0.0888 REMARK 3 S31: -0.0287 S32: 0.0095 S33: -0.0016 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 69 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.0578 -11.5926 28.4655 REMARK 3 T TENSOR REMARK 3 T11: 0.3008 T22: 0.2311 REMARK 3 T33: 0.2263 T12: 0.0053 REMARK 3 T13: 0.0127 T23: 0.0412 REMARK 3 L TENSOR REMARK 3 L11: 0.8184 L22: 0.7540 REMARK 3 L33: 0.2031 L12: 0.0345 REMARK 3 L13: 0.1713 L23: -0.2970 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: -0.2559 S13: 0.2497 REMARK 3 S21: 0.4602 S22: 0.0256 S23: 0.1327 REMARK 3 S31: -0.2737 S32: -0.0711 S33: 0.0397 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 70 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.5379 -7.5961 9.2187 REMARK 3 T TENSOR REMARK 3 T11: 0.1230 T22: 0.1380 REMARK 3 T33: 0.0810 T12: 0.0038 REMARK 3 T13: 0.0058 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.2570 L22: 1.9904 REMARK 3 L33: 1.1076 L12: -0.2143 REMARK 3 L13: 0.3571 L23: -0.7430 REMARK 3 S TENSOR REMARK 3 S11: 0.0102 S12: 0.0475 S13: 0.0087 REMARK 3 S21: -0.1477 S22: -0.0558 S23: -0.0636 REMARK 3 S31: 0.1076 S32: 0.0846 S33: -0.0137 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 213 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9164 8.7575 5.9976 REMARK 3 T TENSOR REMARK 3 T11: 0.1563 T22: 0.1531 REMARK 3 T33: 0.1873 T12: 0.0053 REMARK 3 T13: -0.0004 T23: 0.0276 REMARK 3 L TENSOR REMARK 3 L11: 0.3445 L22: 0.8607 REMARK 3 L33: 0.8252 L12: 0.1200 REMARK 3 L13: 0.0503 L23: -0.9328 REMARK 3 S TENSOR REMARK 3 S11: -0.0586 S12: -0.0226 S13: 0.1651 REMARK 3 S21: 0.2526 S22: -0.0517 S23: -0.0551 REMARK 3 S31: -0.4008 S32: 0.1336 S33: -0.0198 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 214 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.9005 17.9226 -11.4659 REMARK 3 T TENSOR REMARK 3 T11: 0.2125 T22: 0.1887 REMARK 3 T33: 0.3258 T12: -0.0063 REMARK 3 T13: 0.0002 T23: 0.0832 REMARK 3 L TENSOR REMARK 3 L11: 1.0730 L22: 2.0476 REMARK 3 L33: 1.9955 L12: -0.0429 REMARK 3 L13: -1.0665 L23: -1.2903 REMARK 3 S TENSOR REMARK 3 S11: 0.0589 S12: 0.0854 S13: 0.2179 REMARK 3 S21: 0.0548 S22: -0.2078 S23: -0.2208 REMARK 3 S31: -0.0974 S32: 0.1894 S33: -0.0006 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 292 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.9209 20.1746 -7.4808 REMARK 3 T TENSOR REMARK 3 T11: 0.2258 T22: 0.1603 REMARK 3 T33: 0.3739 T12: 0.0187 REMARK 3 T13: 0.0611 T23: 0.0477 REMARK 3 L TENSOR REMARK 3 L11: 0.5351 L22: 0.2517 REMARK 3 L33: 0.8143 L12: -0.1211 REMARK 3 L13: 0.4052 L23: 0.1852 REMARK 3 S TENSOR REMARK 3 S11: 0.0425 S12: -0.0623 S13: 0.4826 REMARK 3 S21: 0.0908 S22: 0.0468 S23: 0.3839 REMARK 3 S31: -0.2037 S32: -0.1471 S33: -0.0028 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 293 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2225 -0.0691 -2.5603 REMARK 3 T TENSOR REMARK 3 T11: 0.3253 T22: 0.2176 REMARK 3 T33: 0.2208 T12: 0.0482 REMARK 3 T13: 0.0110 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 1.0205 L22: 0.7548 REMARK 3 L33: 0.9646 L12: 0.4237 REMARK 3 L13: -0.6475 L23: -0.3245 REMARK 3 S TENSOR REMARK 3 S11: -0.3902 S12: 0.0134 S13: -0.2295 REMARK 3 S21: -0.1947 S22: 0.2536 S23: -0.1542 REMARK 3 S31: 0.3745 S32: -0.1362 S33: -0.0298 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 6YZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1292108593. 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 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 (%): 37.65 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., COUNTER-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: 6320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 753 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 845 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: C 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 PHE A 305 REMARK 465 GLN A 306 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 THR A 304 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 SG CYS A 145 C AR7 C 4 1.41 REMARK 500 SG CYS A 145 C AR7 C 4 1.41 REMARK 500 H GLY A 195 O HOH A 512 1.54 REMARK 500 O HOH A 515 O HOH A 519 1.90 REMARK 500 O THR A 196 O HOH A 501 1.93 REMARK 500 O HOH A 829 O HOH A 847 1.99 REMARK 500 O HOH A 512 O HOH A 563 2.03 REMARK 500 O HOH A 612 O HOH A 762 2.04 REMARK 500 SG CYS A 145 CA AR7 C 4 2.07 REMARK 500 OE1 GLU A 270 O HOH A 502 2.08 REMARK 500 O HOH A 696 O HOH A 808 2.08 REMARK 500 O ALA A 285 O HOH A 503 2.11 REMARK 500 NZ LYS A 61 O HOH A 504 2.13 REMARK 500 SG CYS A 145 CA AR7 C 4 2.13 REMARK 500 O HOH A 588 O HOH A 746 2.17 REMARK 500 OD1 ASP A 48 O HOH A 505 2.18 REMARK 500 O HOH A 779 O HOH A 823 2.18 REMARK 500 OE2 GLU A 288 O HOH A 506 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 669 O HOH A 777 4545 1.95 REMARK 500 O HOH A 787 O HOH A 827 4555 2.11 REMARK 500 O HOH A 833 O HOH A 850 4555 2.15 REMARK 500 O HOH A 571 O HOH A 698 4546 2.16 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 -134.37 53.53 REMARK 500 ASN A 51 74.60 -153.91 REMARK 500 ASN A 84 -118.72 51.14 REMARK 500 TYR A 154 -90.34 45.22 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 DMS 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 IMD 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 CL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for LEUPEPTIN chain C DBREF 6YZ6 A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 6YZ6 C 1 4 PDB 6YZ6 6YZ6 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 C 4 ACE LEU LEU AR7 HET ACE C 1 12 HET AR7 C 4 52 HET DMS A 401 10 HET DMS A 402 10 HET IMD A 403 10 HET DMS A 404 10 HET CL A 405 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 3(C2 H6 O S) FORMUL 5 IMD C3 H5 N2 1+ FORMUL 7 CL CL 1- FORMUL 8 HOH *357(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 PHE A 66 5 6 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 SER A 81 O LYS A 88 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 C 2 LEU C 3 -1 O LEU C 2 N GLU A 166 LINK C AACE C 1 N ALEU C 2 1555 1555 1.46 LINK C BACE C 1 N BLEU C 2 1555 1555 1.45 LINK C ALEU C 3 N AAR7 C 4 1555 1555 1.47 LINK C BLEU C 3 N BAR7 C 4 1555 1555 1.47 SITE 1 AC1 9 GLN A 74 LEU A 75 ARG A 76 PHE A 223 SITE 2 AC1 9 THR A 224 ASP A 263 HOH A 609 HOH A 620 SITE 3 AC1 9 HOH A 778 SITE 1 AC2 1 TYR A 37 SITE 1 AC3 4 HIS A 64 ASN A 65 HOH A 581 HOH A 607 SITE 1 AC4 3 GLY A 15 MET A 17 LYS A 97 SITE 1 AC5 3 SER A 284 ALA A 285 HOH A 550 SITE 1 AC6 18 HIS A 41 ASN A 142 GLY A 143 SER A 144 SITE 2 AC6 18 CYS A 145 HIS A 164 MET A 165 GLU A 166 SITE 3 AC6 18 GLN A 189 THR A 190 GLY A 251 PRO A 252 SITE 4 AC6 18 HOH A 548 HOH C 101 HOH C 102 HOH C 103 SITE 5 AC6 18 HOH C 104 HOH C 105 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