HEADER HYDROLASE 05-MAY-21 7OFT TITLE STRUCTURE OF SARS-COV-2 PAPAIN-LIKE PROTEASE PLPRO IN COMPLEX WITH P- TITLE 2 HYDROXYBENZALDEHYDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE NSP3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3,PL2-PRO,PAPAIN-LIKE COMPND 5 PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.19.12,3.4.22.-; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PAPAIN-LIKE PROTEASE SARS-COV-2 HYDROLASE ZINC BINDING PROTEIN, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SRINIVASAN,N.WERNER,S.FALKE,S.GUENTHER,P.REINKE,H.BROGNARO,N.ULLAH, AUTHOR 2 H.ANDALEEB,M.PERBANDT,B.ALVES FRANCA,M.SCHWINZER,M.WANG,W.EWERT, AUTHOR 3 J.SPRENGER,J.LIESKE,F.KOUA,H.GINN,T.J.LANE,M.WOLF,O.YEFANOV, AUTHOR 4 L.GELISIO,S.SAOUANE,A.TOLSTIKOVA,M.GROESSLER,H.FLECKENSTEIN,F.TROST, AUTHOR 5 K.LORENZEN,R.SCHUBERT,H.HAN,C.SCHMIDT,L.BRINGS,M.GALCHENKOVA, AUTHOR 6 Y.GEVORKOV,C.LI,A.PERK,S.AWEL,A.WAHAB,I.CHOUDARY,D.TURK,W.HINRICHS, AUTHOR 7 H.N.CHAPMAN,A.MEENTS,C.BETZEL REVDAT 4 31-JAN-24 7OFT 1 REMARK REVDAT 3 07-SEP-22 7OFT 1 COMPND JRNL REVDAT 2 24-NOV-21 7OFT 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 FORMUL SHEET LINK CRYST1 REVDAT 2 3 1 ATOM REVDAT 1 12-MAY-21 7OFT 0 JRNL AUTH V.SRINIVASAN,H.BROGNARO,P.R.PRABHU,E.E.DE SOUZA,S.GUNTHER, JRNL AUTH 2 P.Y.A.REINKE,T.J.LANE,H.GINN,H.HAN,W.EWERT,J.SPRENGER, JRNL AUTH 3 F.H.M.KOUA,S.FALKE,N.WERNER,H.ANDALEEB,N.ULLAH,B.A.FRANCA, JRNL AUTH 4 M.WANG,A.L.C.BARRA,M.PERBANDT,M.SCHWINZER,C.SCHMIDT, JRNL AUTH 5 L.BRINGS,K.LORENZEN,R.SCHUBERT,R.R.G.MACHADO,E.D.CANDIDO, JRNL AUTH 6 D.B.L.OLIVEIRA,E.L.DURIGON,S.NIEBLING,A.S.GARCIA,O.YEFANOV, JRNL AUTH 7 J.LIESKE,L.GELISIO,M.DOMARACKY,P.MIDDENDORF,M.GROESSLER, JRNL AUTH 8 F.TROST,M.GALCHENKOVA,A.R.MASHHOUR,S.SAOUANE,J.HAKANPAA, JRNL AUTH 9 M.WOLF,M.G.ALAI,D.TURK,A.R.PEARSON,H.N.CHAPMAN,W.HINRICHS, JRNL AUTH10 C.WRENGER,A.MEENTS,C.BETZEL JRNL TITL ANTIVIRAL ACTIVITY OF NATURAL PHENOLIC COMPOUNDS IN COMPLEX JRNL TITL 2 AT AN ALLOSTERIC SITE OF SARS-COV-2 PAPAIN-LIKE PROTEASE. JRNL REF COMMUN BIOL V. 5 805 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 35953531 JRNL DOI 10.1038/S42003-022-03737-7 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38403 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1931 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 4.7000 - 3.7300 1.00 2660 141 0.1369 0.1527 REMARK 3 2 3.7300 - 3.2600 1.00 2624 137 0.1598 0.2036 REMARK 3 3 3.2600 - 2.9600 1.00 2643 130 0.1970 0.2267 REMARK 3 4 2.9600 - 2.7500 1.00 2603 136 0.2070 0.2653 REMARK 3 5 2.7500 - 2.5900 1.00 2596 139 0.2148 0.2287 REMARK 3 6 2.5900 - 2.4600 1.00 2567 157 0.1984 0.2416 REMARK 3 7 2.4600 - 2.3500 1.00 2570 135 0.2148 0.2368 REMARK 3 8 2.3500 - 2.2600 1.00 2606 135 0.2068 0.2742 REMARK 3 9 2.2600 - 2.1800 1.00 2550 149 0.2276 0.2649 REMARK 3 10 2.1800 - 2.1100 1.00 2572 117 0.2324 0.2685 REMARK 3 11 2.1100 - 2.0500 1.00 2566 134 0.2451 0.2925 REMARK 3 12 2.0500 - 2.0000 1.00 2593 115 0.2521 0.2856 REMARK 3 13 2.0000 - 1.9500 1.00 2548 142 0.2947 0.3595 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.80 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 1:770) REMARK 3 ORIGIN FOR THE GROUP (A): 36.4983 9.5322 16.5104 REMARK 3 T TENSOR REMARK 3 T11: 0.2527 T22: 0.2997 REMARK 3 T33: 0.4308 T12: -0.0005 REMARK 3 T13: 0.0181 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 0.7751 L22: 0.7162 REMARK 3 L33: 1.8937 L12: -0.0717 REMARK 3 L13: 0.2612 L23: 0.0908 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0884 S13: 0.0693 REMARK 3 S21: -0.0530 S22: -0.0773 S23: 0.0115 REMARK 3 S31: 0.1113 S32: -0.0416 S33: 0.0295 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 7OFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292115446. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-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) : 1.033 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38419 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 44.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 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 : 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: 7NFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CO-CRYSTALLIZATION WITH THE COMPOUNDS REMARK 280 WAS ACHIEVED MIXING 0.2 UL OF PROTEIN SOLUTION (22 MG/ML) IN 50 REMARK 280 MM TRIS BUFFER (PH 8.0) CONTAINING 1 MM TCEP AND 150 MM NACL REMARK 280 WITH 0.1 UL OF RESERVOIR SOLUTION CONSISTING OF 1.0M NAH2PO4/ REMARK 280 1.0MKH2PO4, 100MM TRIS_HCL PH=7.5. THIS GROWTH SOLUTION WAS REMARK 280 EQUILIBRATED BY SITTING DROP VAPOR DIFFUSION AGAINST 80 UL REMARK 280 RESERVOIR SOLUTION. PRIOR TO CRYSTALLIZATION 100 NL DROPLETS OF REMARK 280 10 MM COMPOUND SOLUTIONS IN DMSO WERE APPLIED TO THE WELLS OF REMARK 280 SWISSCI 96-WELL PLATES (2-WELL) AND SUBSEQUENTLY DRIED IN REMARK 280 VACUUM., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 89.58533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.79267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.79267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.58533 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 647 O HOH A 686 2.16 REMARK 500 O HOH A 729 O HOH A 756 2.19 REMARK 500 O LEU A 162 O HOH A 501 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 725 O HOH A 725 5555 2.18 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 A 103 -169.33 -110.18 REMARK 500 LYS A 279 -131.33 -118.32 REMARK 500 ASN A 308 -64.96 -138.58 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 K A 412 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 176 O REMARK 620 2 HOH A 591 O 88.2 REMARK 620 3 HOH A 594 O 82.7 109.0 REMARK 620 4 HOH A 621 O 85.8 171.5 76.2 REMARK 620 5 HOH A 685 O 88.3 89.0 159.5 84.8 REMARK 620 6 HOH A 762 O 167.4 96.9 84.8 90.3 103.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 411 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 179 OD1 REMARK 620 2 LYS A 200 O 74.6 REMARK 620 3 GLU A 203 OE2 92.5 21.9 REMARK 620 4 HOH A 555 O 76.2 143.1 165.0 REMARK 620 5 HOH A 685 O 61.5 112.5 112.2 71.2 REMARK 620 6 HOH A 731 O 83.8 21.3 33.6 133.4 132.6 REMARK 620 7 HOH A 762 O 115.8 70.4 49.8 144.3 85.1 82.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 189 SG REMARK 620 2 CYS A 192 SG 119.3 REMARK 620 3 CYS A 224 SG 105.5 107.1 REMARK 620 4 CYS A 226 SG 103.3 111.1 110.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NFV RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 PAPAIN-LIKE PROTEASE PLPRO WITHOUT BOUND REMARK 900 LIGAND REMARK 900 RELATED ID: 7OFS RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 PAPAIN-LIKE PROTEASE PLPRO IN COMPLEX WITH REMARK 900 4-(2-HYDROXYETHYL)PHENOL REMARK 900 RELATED ID: 7OFU RELATED DB: PDB REMARK 900 STRUCTURE OF SARS-COV-2 PAPAIN-LIKE PROTEASE PLPRO IN COMPLEX WITH REMARK 900 3, 4-DIHYDROXYBENZOIC ACID, METHYL ESTER DBREF 7OFT A 1 315 UNP P0DTC1 R1A_SARS2 1564 1878 SEQRES 1 A 315 GLU VAL ARG THR ILE LYS VAL PHE THR THR VAL ASP ASN SEQRES 2 A 315 ILE ASN LEU HIS THR GLN VAL VAL ASP MET SER MET THR SEQRES 3 A 315 TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP GLY ALA SEQRES 4 A 315 ASP VAL THR LYS ILE LYS PRO HIS ASN SER HIS GLU GLY SEQRES 5 A 315 LYS THR PHE TYR VAL LEU PRO ASN ASP ASP THR LEU ARG SEQRES 6 A 315 VAL GLU ALA PHE GLU TYR TYR HIS THR THR ASP PRO SER SEQRES 7 A 315 PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS THR LYS SEQRES 8 A 315 LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU THR SER ILE SEQRES 9 A 315 LYS TRP ALA ASP ASN ASN CYS TYR LEU ALA THR ALA LEU SEQRES 10 A 315 LEU THR LEU GLN GLN ILE GLU LEU LYS PHE ASN PRO PRO SEQRES 11 A 315 ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG ALA GLY GLU SEQRES 12 A 315 ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR CYS ASN SEQRES 13 A 315 LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU THR MET SEQRES 14 A 315 SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SER CYS LYS SEQRES 15 A 315 ARG VAL LEU ASN VAL VAL CYS LYS THR CYS GLY GLN GLN SEQRES 16 A 315 GLN THR THR LEU LYS GLY VAL GLU ALA VAL MET TYR MET SEQRES 17 A 315 GLY THR LEU SER TYR GLU GLN PHE LYS LYS GLY VAL GLN SEQRES 18 A 315 ILE PRO CYS THR CYS GLY LYS GLN ALA THR LYS TYR LEU SEQRES 19 A 315 VAL GLN GLN GLU SER PRO PHE VAL MET MET SER ALA PRO SEQRES 20 A 315 PRO ALA GLN TYR GLU LEU LYS HIS GLY THR PHE THR CYS SEQRES 21 A 315 ALA SER GLU TYR THR GLY ASN TYR GLN CYS GLY HIS TYR SEQRES 22 A 315 LYS HIS ILE THR SER LYS GLU THR LEU TYR CYS ILE ASP SEQRES 23 A 315 GLY ALA LEU LEU THR LYS SER SER GLU TYR LYS GLY PRO SEQRES 24 A 315 ILE THR ASP VAL PHE TYR LYS GLU ASN SER TYR THR THR SEQRES 25 A 315 THR ILE LYS HET ZN A 401 1 HET CL A 402 1 HET CL A 403 1 HET CL A 404 1 HET CL A 405 1 HET CL A 406 1 HET CL A 407 1 HET CL A 408 1 HET CL A 409 1 HET HBA A 410 9 HET K A 411 1 HET K A 412 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM HBA P-HYDROXYBENZALDEHYDE HETNAM K POTASSIUM ION FORMUL 2 ZN ZN 2+ FORMUL 3 CL 8(CL 1-) FORMUL 11 HBA C7 H6 O2 FORMUL 12 K 2(K 1+) FORMUL 14 HOH *270(H2 O) HELIX 1 AA1 THR A 26 GLY A 32 1 7 HELIX 2 AA2 HIS A 47 GLU A 51 5 5 HELIX 3 AA3 ASP A 61 HIS A 73 1 13 HELIX 4 AA4 SER A 78 LYS A 91 1 14 HELIX 5 AA5 ASN A 110 GLN A 121 1 12 HELIX 6 AA6 PRO A 129 ALA A 141 1 13 HELIX 7 AA7 ALA A 144 CYS A 155 1 12 HELIX 8 AA8 ASP A 164 HIS A 175 1 12 HELIX 9 AA9 GLY A 201 VAL A 205 1 5 HELIX 10 AB1 SER A 212 GLY A 219 1 8 SHEET 1 AA1 5 HIS A 17 ASP A 22 0 SHEET 2 AA1 5 THR A 4 THR A 10 -1 N VAL A 7 O GLN A 19 SHEET 3 AA1 5 THR A 54 VAL A 57 1 O PHE A 55 N PHE A 8 SHEET 4 AA1 5 THR A 34 LEU A 36 -1 N TYR A 35 O TYR A 56 SHEET 5 AA1 5 ALA A 39 ASP A 40 -1 O ALA A 39 N LEU A 36 SHEET 1 AA2 2 GLN A 97 VAL A 98 0 SHEET 2 AA2 2 LEU A 101 THR A 102 -1 O LEU A 101 N VAL A 98 SHEET 1 AA3 4 GLY A 193 LYS A 200 0 SHEET 2 AA3 4 LYS A 182 CYS A 189 -1 N LEU A 185 O THR A 197 SHEET 3 AA3 4 GLN A 229 GLU A 238 -1 O THR A 231 N VAL A 188 SHEET 4 AA3 4 VAL A 220 PRO A 223 -1 N ILE A 222 O ALA A 230 SHEET 1 AA4 4 GLY A 193 LYS A 200 0 SHEET 2 AA4 4 LYS A 182 CYS A 189 -1 N LEU A 185 O THR A 197 SHEET 3 AA4 4 GLN A 229 GLU A 238 -1 O THR A 231 N VAL A 188 SHEET 4 AA4 4 SER A 309 THR A 311 -1 O TYR A 310 N GLN A 237 SHEET 1 AA5 7 MET A 206 MET A 208 0 SHEET 2 AA5 7 PHE A 241 LYS A 254 1 O SER A 245 N TYR A 207 SHEET 3 AA5 7 GLU A 295 LYS A 306 -1 O TYR A 296 N LEU A 253 SHEET 4 AA5 7 CYS A 260 GLY A 266 -1 N CYS A 260 O PHE A 304 SHEET 5 AA5 7 GLY A 271 SER A 278 -1 O LYS A 274 N GLU A 263 SHEET 6 AA5 7 LEU A 282 ASP A 286 -1 O ILE A 285 N HIS A 275 SHEET 7 AA5 7 LEU A 289 SER A 293 -1 O LEU A 289 N ASP A 286 LINK O ALA A 176 K K A 412 1555 1555 2.63 LINK OD1 ASP A 179 K K A 411 1555 1555 2.79 LINK SG CYS A 189 ZN ZN A 401 1555 1555 2.41 LINK SG CYS A 192 ZN ZN A 401 1555 1555 2.50 LINK O LYS A 200 K K A 411 1555 5555 2.66 LINK OE2 GLU A 203 K K A 411 1555 5555 2.81 LINK SG CYS A 224 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 226 ZN ZN A 401 1555 1555 2.39 LINK K K A 411 O HOH A 555 1555 1555 2.81 LINK K K A 411 O HOH A 685 1555 1555 3.25 LINK K K A 411 O HOH A 731 1555 1555 2.80 LINK K K A 411 O HOH A 762 1555 1555 2.85 LINK K K A 412 O HOH A 591 1555 1555 2.56 LINK K K A 412 O HOH A 594 1555 1555 2.38 LINK K K A 412 O HOH A 621 1555 1555 2.78 LINK K K A 412 O HOH A 685 1555 1555 2.63 LINK K K A 412 O HOH A 762 1555 1555 2.64 CRYST1 81.613 81.613 134.378 90.00 90.00 120.00 P 32 2 1 6 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 0.012253 0.007074 0.000000 0.00000 SCALE2 0.000000 0.014148 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007442 0.00000