HEADER HYDROLASE/HYDROLASE INHIBITOR 09-MAY-20 6WX4 TITLE CRYSTAL STRUCTURE OF THE SARS COV-2 PAPAIN-LIKE PROTEASE IN COMPLEX TITLE 2 WITH PEPTIDE INHIBITOR VIR251 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: D; COMPND 4 SYNONYM: PAPAIN-LIKE PROTEASE,PP1AB,ORF1AB POLYPROTEIN,NSP3,PL2-PRO, COMPND 5 PAPAIN-LIKE PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.19.121, 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VIR251; COMPND 10 CHAIN: I; 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 BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: CODON PLUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET29B; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32360 KEYWDS COVID-19, CORONAVIRUS, SARS, COV-2, PAPAIN-LIKE PROTEASE, PLPRO, KEYWDS 2 DEUBIQUITINATING ENZYME, UBIQUITIN, ACTIVITY-BASED PROBE, HYDROLASE- KEYWDS 3 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.LV,S.K.OLSEN REVDAT 6 15-NOV-23 6WX4 1 LINK ATOM REVDAT 5 18-OCT-23 6WX4 1 JRNL REVDAT 4 27-JAN-21 6WX4 1 COMPND REVDAT 3 02-DEC-20 6WX4 1 JRNL REVDAT 2 24-JUN-20 6WX4 1 JRNL REVDAT 1 20-MAY-20 6WX4 0 JRNL AUTH W.RUT,Z.LV,M.ZMUDZINSKI,S.PATCHETT,D.NAYAK,S.J.SNIPAS, JRNL AUTH 2 F.EL OUALID,T.T.HUANG,M.BEKES,M.DRAG,S.K.OLSEN JRNL TITL ACTIVITY PROFILING AND CRYSTAL STRUCTURES OF INHIBITOR-BOUND JRNL TITL 2 SARS-COV-2 PAPAIN-LIKE PROTEASE: A FRAMEWORK FOR JRNL TITL 3 ANTI-COVID-19 DRUG DESIGN. JRNL REF SCI ADV V. 6 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 33067239 JRNL DOI 10.1126/SCIADV.ABD4596 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.RUT,Z.LV,M.ZMUDZINSKI,S.PATCHETT,D.NAYAK,S.J.SNIPAS, REMARK 1 AUTH 2 F.EL OUALID,T.T.HUANG,M.BEKES,M.DRAG,S.K.OLSEN REMARK 1 TITL ACTIVITY PROFILING AND STRUCTURES OF INHIBITOR-BOUND REMARK 1 TITL 2 SARS-COV-2-PLPRO PROTEASE PROVIDES A FRAMEWORK FOR REMARK 1 TITL 3 ANTI-COVID-19 DRUG DESIGN. REMARK 1 REF BIORXIV 2020 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 32511411 REMARK 1 DOI 10.1101/2020.04.29.068890 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 46301 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.320 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 90.7000 - 3.9889 1.00 3373 153 0.1554 0.1829 REMARK 3 2 3.9889 - 3.1660 1.00 3243 145 0.1579 0.1831 REMARK 3 3 3.1660 - 2.7658 1.00 3190 145 0.1834 0.1932 REMARK 3 4 2.7658 - 2.5129 1.00 3197 145 0.1885 0.2150 REMARK 3 5 2.5129 - 2.3328 1.00 3178 143 0.1793 0.2070 REMARK 3 6 2.3328 - 2.1952 1.00 3169 143 0.1714 0.2268 REMARK 3 7 2.1952 - 2.0853 1.00 3169 143 0.1645 0.1771 REMARK 3 8 2.0853 - 1.9945 1.00 3137 142 0.1593 0.1753 REMARK 3 9 1.9945 - 1.9177 1.00 3164 142 0.1637 0.2134 REMARK 3 10 1.9177 - 1.8515 1.00 3123 141 0.1809 0.2294 REMARK 3 11 1.8515 - 1.7936 1.00 3115 141 0.1950 0.2186 REMARK 3 12 1.7936 - 1.7424 1.00 3165 143 0.2001 0.2303 REMARK 3 13 1.7424 - 1.6965 1.00 3145 141 0.2164 0.2149 REMARK 3 14 1.6965 - 1.6551 0.94 2933 133 0.2407 0.2575 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.69 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 : 0.006 2646 REMARK 3 ANGLE : 0.844 3581 REMARK 3 CHIRALITY : 0.049 394 REMARK 3 PLANARITY : 0.005 457 REMARK 3 DIHEDRAL : 11.852 1557 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 78 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.8584 -11.2780 -14.0916 REMARK 3 T TENSOR REMARK 3 T11: 0.3251 T22: 0.3506 REMARK 3 T33: 0.3134 T12: 0.0123 REMARK 3 T13: 0.0177 T23: -0.0422 REMARK 3 L TENSOR REMARK 3 L11: 0.5245 L22: 0.1438 REMARK 3 L33: 2.2132 L12: -0.1752 REMARK 3 L13: -1.0808 L23: -0.4358 REMARK 3 S TENSOR REMARK 3 S11: -0.0851 S12: -0.1137 S13: 0.0327 REMARK 3 S21: 0.1576 S22: -0.1168 S23: 0.2863 REMARK 3 S31: -0.1612 S32: -0.1082 S33: -0.0021 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 79 THROUGH 175 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.4659 -13.7040 -32.6477 REMARK 3 T TENSOR REMARK 3 T11: 0.1988 T22: 0.1949 REMARK 3 T33: 0.2373 T12: 0.0074 REMARK 3 T13: -0.0303 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 1.5677 L22: 1.2118 REMARK 3 L33: 1.7672 L12: -0.2905 REMARK 3 L13: -0.8826 L23: 0.2411 REMARK 3 S TENSOR REMARK 3 S11: 0.0298 S12: -0.0705 S13: 0.0893 REMARK 3 S21: -0.0451 S22: -0.0103 S23: -0.0354 REMARK 3 S31: -0.0252 S32: 0.0209 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 176 THROUGH 228 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.9160 -22.8573 -59.9614 REMARK 3 T TENSOR REMARK 3 T11: 0.3779 T22: 0.3633 REMARK 3 T33: 0.2936 T12: 0.0183 REMARK 3 T13: -0.0564 T23: -0.0535 REMARK 3 L TENSOR REMARK 3 L11: 0.5902 L22: 0.6141 REMARK 3 L33: 0.7739 L12: 0.0199 REMARK 3 L13: 0.2977 L23: 0.0719 REMARK 3 S TENSOR REMARK 3 S11: -0.0727 S12: 0.0717 S13: -0.2218 REMARK 3 S21: -0.1561 S22: -0.0584 S23: 0.0870 REMARK 3 S31: -0.0391 S32: -0.2431 S33: -0.0083 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 229 THROUGH 320 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.5523 -17.2123 -51.7144 REMARK 3 T TENSOR REMARK 3 T11: 0.3161 T22: 0.2369 REMARK 3 T33: 0.2731 T12: -0.0152 REMARK 3 T13: 0.0007 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 0.8389 L22: 0.3820 REMARK 3 L33: 2.2939 L12: -0.0417 REMARK 3 L13: 0.5363 L23: 0.9524 REMARK 3 S TENSOR REMARK 3 S11: -0.0867 S12: 0.0479 S13: 0.0794 REMARK 3 S21: -0.2464 S22: 0.0053 S23: -0.2079 REMARK 3 S31: -0.3203 S32: 0.1483 S33: -0.0055 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 6WX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000249136. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46470 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 90.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 1.73200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 6WUU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1 M TRIS HCL PH 8.5 AND 0.5% W/V POLYETHYLENE REMARK 280 GLYCOL MONOMETHYL ETHER 5,000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.43450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.74100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.52400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.43450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.74100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.52400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.43450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.74100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.52400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.43450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.74100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.52400 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: D, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 615 LIES ON A SPECIAL POSITION. REMARK 375 HOH D 752 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 PEPTIDE COVALENTLY LINKED TO ACTIVE SITE CYS REMARK 400 REMARK 400 THE VIR251PAPAIN-LIKE PROTEASE PEPTIDE INHIBITOR IS PEPTIDE-LIKE, A REMARK 400 MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: VIR251PAPAIN-LIKE PROTEASE PEPTIDE INHIBITOR REMARK 400 CHAIN: I 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 MET D -1 REMARK 465 ARG D 0 REMARK 465 HIS D 321 REMARK 465 HIS D 322 REMARK 465 HIS D 323 REMARK 465 HIS D 324 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 D 616 O HOH D 767 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 SER D 103 -168.43 -111.82 REMARK 500 GLU D 143 77.63 -106.82 REMARK 500 CYS D 270 85.40 -153.16 REMARK 500 LYS D 279 -126.49 -118.03 REMARK 500 ASN D 308 -66.10 -139.05 REMARK 500 GLU D 318 -175.25 -66.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 189 SG REMARK 620 2 CYS D 192 SG 106.4 REMARK 620 3 CYS D 224 SG 108.3 116.2 REMARK 620 4 CYS D 226 SG 115.9 109.8 100.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues ACY A 1 and 73O A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues 73O A 2 and DPP A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6WUU RELATED DB: PDB REMARK 900 THIS IS THE SAME ENZYME IN COMPLEX WITH A DIFFERENT INHIBITOR. I REMARK 900 WOULD LIKE TO RELEASE THESE COORDINATES TOGETHER AND I CAN CHANGE REMARK 900 TO RELEASE IMMEDIATELY AS LONG AS THEY RELEASE TOGETHER. DBREF 6WX4 D 0 316 UNP P0DTD1 R1AB_SARS2 1563 1879 DBREF 6WX4 I 1 5 PDB 6WX4 6WX4 1 5 SEQADV 6WX4 MET D -1 UNP P0DTD1 INITIATING METHIONINE SEQADV 6WX4 LEU D 317 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 GLU D 318 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 319 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 320 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 321 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 322 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 323 UNP P0DTD1 EXPRESSION TAG SEQADV 6WX4 HIS D 324 UNP P0DTD1 EXPRESSION TAG SEQRES 1 D 326 MET ARG GLU VAL ARG THR ILE LYS VAL PHE THR THR VAL SEQRES 2 D 326 ASP ASN ILE ASN LEU HIS THR GLN VAL VAL ASP MET SER SEQRES 3 D 326 MET THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP SEQRES 4 D 326 GLY ALA ASP VAL THR LYS ILE LYS PRO HIS ASN SER HIS SEQRES 5 D 326 GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ASP ASP THR SEQRES 6 D 326 LEU ARG VAL GLU ALA PHE GLU TYR TYR HIS THR THR ASP SEQRES 7 D 326 PRO SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS SEQRES 8 D 326 THR LYS LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU THR SEQRES 9 D 326 SER ILE LYS TRP ALA ASP ASN ASN CYS TYR LEU ALA THR SEQRES 10 D 326 ALA LEU LEU THR LEU GLN GLN ILE GLU LEU LYS PHE ASN SEQRES 11 D 326 PRO PRO ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG ALA SEQRES 12 D 326 GLY GLU ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR SEQRES 13 D 326 CYS ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU SEQRES 14 D 326 THR MET SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SER SEQRES 15 D 326 CYS LYS ARG VAL LEU ASN VAL VAL CYS LYS THR CYS GLY SEQRES 16 D 326 GLN GLN GLN THR THR LEU LYS GLY VAL GLU ALA VAL MET SEQRES 17 D 326 TYR MET GLY THR LEU SER TYR GLU GLN PHE LYS LYS GLY SEQRES 18 D 326 VAL GLN ILE PRO CYS THR CYS GLY LYS GLN ALA THR LYS SEQRES 19 D 326 TYR LEU VAL GLN GLN GLU SER PRO PHE VAL MET MET SER SEQRES 20 D 326 ALA PRO PRO ALA GLN TYR GLU LEU LYS HIS GLY THR PHE SEQRES 21 D 326 THR CYS ALA SER GLU TYR THR GLY ASN TYR GLN CYS GLY SEQRES 22 D 326 HIS TYR LYS HIS ILE THR SER LYS GLU THR LEU TYR CYS SEQRES 23 D 326 ILE ASP GLY ALA LEU LEU THR LYS SER SER GLU TYR LYS SEQRES 24 D 326 GLY PRO ILE THR ASP VAL PHE TYR LYS GLU ASN SER TYR SEQRES 25 D 326 THR THR THR ILE LYS PRO LEU GLU HIS HIS HIS HIS HIS SEQRES 26 D 326 HIS SEQRES 1 I 5 ACY 73O DPP GLY GVE HET ACY I 1 3 HET 73O I 2 13 HET DPP I 3 6 HET GVE I 5 8 HET ZN D 501 1 HETNAM ACY ACETIC ACID HETNAM 73O (2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID HETNAM DPP DIAMINOPROPANOIC ACID HETNAM GVE METHYL 4-AMINOBUTANOATE HETNAM ZN ZINC ION FORMUL 2 ACY C2 H4 O2 FORMUL 2 73O C10 H13 N O3 FORMUL 2 DPP C3 H8 N2 O2 FORMUL 2 GVE C5 H11 N O2 FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *194(H2 O) HELIX 1 AA1 THR D 26 GLY D 32 1 7 HELIX 2 AA2 HIS D 47 GLU D 51 5 5 HELIX 3 AA3 ASP D 61 HIS D 73 1 13 HELIX 4 AA4 SER D 78 LYS D 91 1 14 HELIX 5 AA5 ASN D 110 GLN D 121 1 12 HELIX 6 AA6 PRO D 129 ALA D 141 1 13 HELIX 7 AA7 ALA D 144 ASN D 156 1 13 HELIX 8 AA8 ASP D 164 GLN D 174 1 11 HELIX 9 AA9 GLY D 201 VAL D 205 1 5 HELIX 10 AB1 SER D 212 GLY D 219 1 8 SHEET 1 AA1 5 HIS D 17 ASP D 22 0 SHEET 2 AA1 5 THR D 4 THR D 10 -1 N VAL D 7 O GLN D 19 SHEET 3 AA1 5 THR D 54 VAL D 57 1 O PHE D 55 N PHE D 8 SHEET 4 AA1 5 THR D 34 LEU D 36 -1 N TYR D 35 O TYR D 56 SHEET 5 AA1 5 ALA D 39 ASP D 40 -1 O ALA D 39 N LEU D 36 SHEET 1 AA2 2 GLN D 97 VAL D 98 0 SHEET 2 AA2 2 LEU D 101 THR D 102 -1 O LEU D 101 N VAL D 98 SHEET 1 AA3 4 GLY D 193 LYS D 200 0 SHEET 2 AA3 4 LYS D 182 CYS D 189 -1 N ARG D 183 O LEU D 199 SHEET 3 AA3 4 GLN D 229 GLU D 238 -1 O THR D 231 N VAL D 188 SHEET 4 AA3 4 VAL D 220 PRO D 223 -1 N ILE D 222 O ALA D 230 SHEET 1 AA4 4 GLY D 193 LYS D 200 0 SHEET 2 AA4 4 LYS D 182 CYS D 189 -1 N ARG D 183 O LEU D 199 SHEET 3 AA4 4 GLN D 229 GLU D 238 -1 O THR D 231 N VAL D 188 SHEET 4 AA4 4 SER D 309 THR D 311 -1 O TYR D 310 N GLN D 237 SHEET 1 AA5 7 MET D 206 MET D 208 0 SHEET 2 AA5 7 PHE D 241 LEU D 253 1 O SER D 245 N TYR D 207 SHEET 3 AA5 7 TYR D 296 LYS D 306 -1 O VAL D 303 N MET D 244 SHEET 4 AA5 7 CYS D 260 ASN D 267 -1 N CYS D 260 O PHE D 304 SHEET 5 AA5 7 CYS D 270 SER D 278 -1 O ILE D 276 N ALA D 261 SHEET 6 AA5 7 LEU D 282 ASP D 286 -1 O ILE D 285 N HIS D 275 SHEET 7 AA5 7 LEU D 289 SER D 293 -1 O LEU D 289 N ASP D 286 LINK SG CYS D 111 CB GVE I 5 1555 1555 1.79 LINK C ACY I 1 N 73O I 2 1555 1555 1.45 LINK C 73O I 2 N DPP I 3 1555 1555 1.44 LINK C DPP I 3 N GLY I 4 1555 1555 1.43 LINK C GLY I 4 N GVE I 5 1555 1555 1.44 LINK SG CYS D 189 ZN ZN D 501 1555 1555 2.36 LINK SG CYS D 192 ZN ZN D 501 1555 1555 2.34 LINK SG CYS D 224 ZN ZN D 501 1555 1555 2.40 LINK SG CYS D 226 ZN ZN D 501 1555 1555 2.28 SITE 1 AC1 4 CYS D 189 CYS D 192 CYS D 224 CYS D 226 SITE 1 AC2 13 DPP I 3 HOH I 101 HOH I 102 ASP D 76 SITE 2 AC2 13 ARG D 82 ASN D 156 GLY D 163 ASP D 164 SITE 3 AC2 13 PRO D 248 TYR D 264 TYR D 268 TYR D 273 SITE 4 AC2 13 HOH D 647 SITE 1 AC3 15 ACY I 1 GLY I 4 HOH I 101 ASP D 76 SITE 2 AC3 15 ARG D 82 ASN D 156 GLY D 163 ASP D 164 SITE 3 AC3 15 PRO D 248 TYR D 264 TYR D 268 GLN D 269 SITE 4 AC3 15 GLY D 271 TYR D 273 HOH D 743 CRYST1 44.869 113.482 151.048 90.00 90.00 90.00 I 2 2 2 8 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 0.022287 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006620 0.00000