HEADER HYDROLASE 15-MAR-21 7M1Y TITLE THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2, C111S TITLE 2 MUTANT, IN COMPLEX WITH EBSELEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3, NSP3, PL2-PRO, PAPAIN-LIKE COMPND 5 PROTEINASE, PL-PRO; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: THREE N-TERMINAL RESIDUES (SNA) ARE EXPRESSION TAG 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG53 KEYWDS COVID-19, CORONAVIRUS, SARS, COV-2, PAPAIN-LIKE PROTEASE, IDP51000, KEYWDS 2 IDP52003, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, KEYWDS 3 CSGID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.OSIPIUK,C.TESAR,M.ENDRES,N.MALTSEVA,A.JOACHIMIAK,CENTER FOR AUTHOR 2 STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 3 25-OCT-23 7M1Y 1 REMARK REVDAT 2 05-APR-23 7M1Y 1 COMPND HETNAM HETSYN REVDAT 1 24-MAR-21 7M1Y 0 JRNL AUTH J.OSIPIUK,C.TESAR,M.ENDRES,N.MALTSEVA,A.JOACHIMIAK, JRNL AUTH 2 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 3 (CSGID) JRNL TITL THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2, JRNL TITL 2 C111S MUTANT, IN COMPLEX WITH EBSELEN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 61978 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3276 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4498 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 220 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4969 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -3.09000 REMARK 3 B12 (A**2) : 0.48000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.138 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.126 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.097 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5252 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4844 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7140 ; 1.614 ; 1.659 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11206 ; 1.332 ; 1.579 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 660 ; 6.219 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 251 ;41.252 ;24.104 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 897 ;16.365 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;15.058 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 699 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6006 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1222 ; 0.001 ; 0.020 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 315 REMARK 3 RESIDUE RANGE : A 501 A 514 REMARK 3 RESIDUE RANGE : B 401 B 402 REMARK 3 ORIGIN FOR THE GROUP (A): 56.264 26.412 40.753 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.0538 REMARK 3 T33: 0.0258 T12: 0.0303 REMARK 3 T13: 0.0110 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.8475 L22: 1.4813 REMARK 3 L33: 0.6732 L12: 0.7577 REMARK 3 L13: -0.1761 L23: -0.4578 REMARK 3 S TENSOR REMARK 3 S11: -0.0475 S12: 0.1500 S13: 0.0011 REMARK 3 S21: -0.0167 S22: 0.0553 S23: 0.1532 REMARK 3 S31: -0.0698 S32: 0.0431 S33: -0.0078 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 314 REMARK 3 RESIDUE RANGE : B 403 B 413 REMARK 3 ORIGIN FOR THE GROUP (A): 32.065 33.728 4.477 REMARK 3 T TENSOR REMARK 3 T11: 0.0597 T22: 0.1404 REMARK 3 T33: 0.0656 T12: 0.0591 REMARK 3 T13: -0.0146 T23: -0.0666 REMARK 3 L TENSOR REMARK 3 L11: 0.8568 L22: 0.9796 REMARK 3 L33: 0.9110 L12: -0.0803 REMARK 3 L13: 0.0387 L23: -0.0322 REMARK 3 S TENSOR REMARK 3 S11: -0.0454 S12: 0.1179 S13: -0.1776 REMARK 3 S21: 0.1575 S22: 0.0803 S23: -0.0101 REMARK 3 S31: 0.0552 S32: 0.0310 S33: -0.0349 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 7M1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65358 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 49.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.60 REMARK 200 R MERGE FOR SHELL (I) : 3.05200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 6WRH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-CL, PH 8.5, 3.5 M SODIUM REMARK 280 FORMATE, 0.1 M SODIUM IODIDE, 4 MM EBSELEN, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 168.54667 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 84.27333 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 126.41000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.13667 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 210.68333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 168.54667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 84.27333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 42.13667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 126.41000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 210.68333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 GLU A 1 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 GLU B 1 REMARK 465 VAL B 2 REMARK 465 LYS B 315 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 OE2 GLU A 263 OH TYR A 296 2.06 REMARK 500 OE2 GLU B 263 OH TYR B 296 2.19 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 PRO A 59 96.02 -68.60 REMARK 500 LYS A 190 -8.08 -54.61 REMARK 500 LYS A 279 -125.53 -109.80 REMARK 500 ASN A 308 -68.66 -138.85 REMARK 500 ASN B 13 19.39 57.67 REMARK 500 ILE B 14 -54.26 -120.22 REMARK 500 TYR B 95 76.98 -116.55 REMARK 500 ASN B 99 52.69 38.01 REMARK 500 ALA B 107 138.87 -171.51 REMARK 500 LYS B 279 -136.43 -128.62 REMARK 500 ASN B 308 -66.57 -143.11 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 NA A 514 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 120 O REMARK 620 2 ILE A 123 O 78.3 REMARK 620 3 TYR A 136 OH 65.6 137.9 REMARK 620 4 HOH A 628 O 73.5 61.1 87.4 REMARK 620 5 HOH A 700 O 145.3 77.4 121.9 73.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 189 SG REMARK 620 2 CYS A 192 SG 116.4 REMARK 620 3 CYS A 224 SG 114.9 110.4 REMARK 620 4 CYS A 226 SG 91.8 103.3 118.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 413 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU B 120 O REMARK 620 2 ILE B 123 O 92.9 REMARK 620 3 TYR B 136 OH 82.6 159.6 REMARK 620 4 HOH B 588 O 111.6 83.3 80.0 REMARK 620 5 HOH B 592 O 160.6 89.7 101.1 87.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 189 SG REMARK 620 2 CYS B 192 SG 113.0 REMARK 620 3 CYS B 224 SG 112.5 102.6 REMARK 620 4 CYS B 226 SG 108.5 109.5 110.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6WZU RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 REMARK 900 RELATED ID: 6WRH RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2, C111S REMARK 900 MUTANT REMARK 900 RELATED ID: CSGID-IDP52003 RELATED DB: TARGETTRACK DBREF 7M1Y A 1 315 UNP P0DTC1 R1A_SARS2 1564 1878 DBREF 7M1Y B 1 315 UNP P0DTC1 R1A_SARS2 1564 1878 SEQADV 7M1Y SER A -2 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y ASN A -1 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y ALA A 0 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y SER A 111 UNP P0DTC1 CYS 1674 ENGINEERED MUTATION SEQADV 7M1Y SER B -2 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y ASN B -1 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y ALA B 0 UNP P0DTC1 EXPRESSION TAG SEQADV 7M1Y SER B 111 UNP P0DTC1 CYS 1674 ENGINEERED MUTATION SEQRES 1 A 318 SER ASN ALA GLU VAL ARG THR ILE LYS VAL PHE THR THR SEQRES 2 A 318 VAL ASP ASN ILE ASN LEU HIS THR GLN VAL VAL ASP MET SEQRES 3 A 318 SER MET THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU SEQRES 4 A 318 ASP GLY ALA ASP VAL THR LYS ILE LYS PRO HIS ASN SER SEQRES 5 A 318 HIS GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ASP ASP SEQRES 6 A 318 THR LEU ARG VAL GLU ALA PHE GLU TYR TYR HIS THR THR SEQRES 7 A 318 ASP PRO SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN SEQRES 8 A 318 HIS THR LYS LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU SEQRES 9 A 318 THR SER ILE LYS TRP ALA ASP ASN ASN SER TYR LEU ALA SEQRES 10 A 318 THR ALA LEU LEU THR LEU GLN GLN ILE GLU LEU LYS PHE SEQRES 11 A 318 ASN PRO PRO ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG SEQRES 12 A 318 ALA GLY GLU ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA SEQRES 13 A 318 TYR CYS ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG SEQRES 14 A 318 GLU THR MET SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SEQRES 15 A 318 SER CYS LYS ARG VAL LEU ASN VAL VAL CYS LYS THR CYS SEQRES 16 A 318 GLY GLN GLN GLN THR THR LEU LYS GLY VAL GLU ALA VAL SEQRES 17 A 318 MET TYR MET GLY THR LEU SER TYR GLU GLN PHE LYS LYS SEQRES 18 A 318 GLY VAL GLN ILE PRO CYS THR CYS GLY LYS GLN ALA THR SEQRES 19 A 318 LYS TYR LEU VAL GLN GLN GLU SER PRO PHE VAL MET MET SEQRES 20 A 318 SER ALA PRO PRO ALA GLN TYR GLU LEU LYS HIS GLY THR SEQRES 21 A 318 PHE THR CYS ALA SER GLU TYR THR GLY ASN TYR GLN CYS SEQRES 22 A 318 GLY HIS TYR LYS HIS ILE THR SER LYS GLU THR LEU TYR SEQRES 23 A 318 CYS ILE ASP GLY ALA LEU LEU THR LYS SER SER GLU TYR SEQRES 24 A 318 LYS GLY PRO ILE THR ASP VAL PHE TYR LYS GLU ASN SER SEQRES 25 A 318 TYR THR THR THR ILE LYS SEQRES 1 B 318 SER ASN ALA GLU VAL ARG THR ILE LYS VAL PHE THR THR SEQRES 2 B 318 VAL ASP ASN ILE ASN LEU HIS THR GLN VAL VAL ASP MET SEQRES 3 B 318 SER MET THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU SEQRES 4 B 318 ASP GLY ALA ASP VAL THR LYS ILE LYS PRO HIS ASN SER SEQRES 5 B 318 HIS GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ASP ASP SEQRES 6 B 318 THR LEU ARG VAL GLU ALA PHE GLU TYR TYR HIS THR THR SEQRES 7 B 318 ASP PRO SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN SEQRES 8 B 318 HIS THR LYS LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU SEQRES 9 B 318 THR SER ILE LYS TRP ALA ASP ASN ASN SER TYR LEU ALA SEQRES 10 B 318 THR ALA LEU LEU THR LEU GLN GLN ILE GLU LEU LYS PHE SEQRES 11 B 318 ASN PRO PRO ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG SEQRES 12 B 318 ALA GLY GLU ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA SEQRES 13 B 318 TYR CYS ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG SEQRES 14 B 318 GLU THR MET SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SEQRES 15 B 318 SER CYS LYS ARG VAL LEU ASN VAL VAL CYS LYS THR CYS SEQRES 16 B 318 GLY GLN GLN GLN THR THR LEU LYS GLY VAL GLU ALA VAL SEQRES 17 B 318 MET TYR MET GLY THR LEU SER TYR GLU GLN PHE LYS LYS SEQRES 18 B 318 GLY VAL GLN ILE PRO CYS THR CYS GLY LYS GLN ALA THR SEQRES 19 B 318 LYS TYR LEU VAL GLN GLN GLU SER PRO PHE VAL MET MET SEQRES 20 B 318 SER ALA PRO PRO ALA GLN TYR GLU LEU LYS HIS GLY THR SEQRES 21 B 318 PHE THR CYS ALA SER GLU TYR THR GLY ASN TYR GLN CYS SEQRES 22 B 318 GLY HIS TYR LYS HIS ILE THR SER LYS GLU THR LEU TYR SEQRES 23 B 318 CYS ILE ASP GLY ALA LEU LEU THR LYS SER SER GLU TYR SEQRES 24 B 318 LYS GLY PRO ILE THR ASP VAL PHE TYR LYS GLU ASN SER SEQRES 25 B 318 TYR THR THR THR ILE LYS HET 9JT A 501 16 HET ZN A 502 1 HET CL A 503 1 HET GOL A 504 6 HET IOD A 505 1 HET IOD A 506 1 HET IOD A 507 1 HET IOD A 508 1 HET IOD A 509 1 HET IOD A 510 1 HET FMT A 511 3 HET FMT A 512 3 HET FMT A 513 3 HET NA A 514 1 HET IOD B 401 1 HET IOD B 402 1 HET 9JT B 403 16 HET ZN B 404 1 HET CL B 405 1 HET GOL B 406 6 HET IOD B 407 1 HET IOD B 408 1 HET IOD B 409 1 HET IOD B 410 1 HET IOD B 411 1 HET FMT B 412 3 HET NA B 413 1 HETNAM 9JT N-PHENYL-2-SELANYLBENZAMIDE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM IOD IODIDE ION HETNAM FMT FORMIC ACID HETNAM NA SODIUM ION HETSYN 9JT ~{N}-PHENYL-2-SELANYL-BENZAMIDE; EBSELEN, BOUND FORM HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 9JT 2(C13 H11 N O SE) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 CL 2(CL 1-) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 7 IOD 13(I 1-) FORMUL 13 FMT 4(C H2 O2) FORMUL 16 NA 2(NA 1+) FORMUL 30 HOH *234(H2 O) HELIX 1 AA1 TYR A 27 GLY A 32 1 6 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 GLY A 142 1 14 HELIX 7 AA7 ALA A 144 ASN A 156 1 13 HELIX 8 AA8 ASP A 164 HIS A 175 1 12 HELIX 9 AA9 VAL A 202 ALA A 204 5 3 HELIX 10 AB1 SER A 212 GLY A 219 1 8 HELIX 11 AB2 TYR B 27 GLY B 32 1 6 HELIX 12 AB3 HIS B 47 GLU B 51 5 5 HELIX 13 AB4 ASP B 61 HIS B 73 1 13 HELIX 14 AB5 SER B 78 LYS B 91 1 14 HELIX 15 AB6 ASN B 110 GLN B 121 1 12 HELIX 16 AB7 PRO B 129 GLY B 142 1 14 HELIX 17 AB8 ALA B 144 ASN B 156 1 13 HELIX 18 AB9 ASP B 164 GLN B 174 1 11 HELIX 19 AC1 VAL B 202 ALA B 204 5 3 HELIX 20 AC2 SER B 212 GLY B 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 THR A 9 O HIS A 17 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 ARG A 183 O LEU A 199 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 ARG A 183 O LEU A 199 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 VAL A 303 N MET A 244 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 THR A 291 N CYS A 284 SHEET 1 AA6 5 HIS B 17 ASP B 22 0 SHEET 2 AA6 5 THR B 4 THR B 10 -1 N ILE B 5 O VAL B 21 SHEET 3 AA6 5 THR B 54 VAL B 57 1 O PHE B 55 N PHE B 8 SHEET 4 AA6 5 THR B 34 LEU B 36 -1 N TYR B 35 O TYR B 56 SHEET 5 AA6 5 ALA B 39 ASP B 40 -1 O ALA B 39 N LEU B 36 SHEET 1 AA7 2 GLN B 97 VAL B 98 0 SHEET 2 AA7 2 LEU B 101 THR B 102 -1 O LEU B 101 N VAL B 98 SHEET 1 AA8 4 GLY B 193 LYS B 200 0 SHEET 2 AA8 4 LYS B 182 CYS B 189 -1 N LEU B 185 O THR B 197 SHEET 3 AA8 4 GLN B 229 GLU B 238 -1 O THR B 231 N VAL B 188 SHEET 4 AA8 4 VAL B 220 PRO B 223 -1 N ILE B 222 O ALA B 230 SHEET 1 AA9 4 GLY B 193 LYS B 200 0 SHEET 2 AA9 4 LYS B 182 CYS B 189 -1 N LEU B 185 O THR B 197 SHEET 3 AA9 4 GLN B 229 GLU B 238 -1 O THR B 231 N VAL B 188 SHEET 4 AA9 4 SER B 309 THR B 311 -1 O TYR B 310 N GLN B 237 SHEET 1 AB1 7 MET B 206 MET B 208 0 SHEET 2 AB1 7 PHE B 241 LEU B 253 1 O SER B 245 N TYR B 207 SHEET 3 AB1 7 TYR B 296 LYS B 306 -1 O VAL B 303 N MET B 244 SHEET 4 AB1 7 CYS B 260 GLY B 266 -1 N CYS B 260 O PHE B 304 SHEET 5 AB1 7 GLY B 271 SER B 278 -1 O LYS B 274 N GLU B 263 SHEET 6 AB1 7 LEU B 282 ASP B 286 -1 O TYR B 283 N THR B 277 SHEET 7 AB1 7 LEU B 289 SER B 293 -1 O THR B 291 N CYS B 284 SSBOND 1 CYS A 270 CYS A 270 1555 10665 2.11 SSBOND 2 CYS B 270 CYS B 270 1555 10665 2.07 LINK O LEU A 120 NA NA A 514 1555 1555 2.46 LINK O ILE A 123 NA NA A 514 1555 1555 2.61 LINK OH TYR A 136 NA NA A 514 1555 1555 2.77 LINK SG CYS A 189 ZN ZN A 502 1555 1555 2.46 LINK SG CYS A 192 ZN ZN A 502 1555 1555 2.38 LINK SG CYS A 224 ZN ZN A 502 1555 1555 1.97 LINK SG CYS A 226 ZN ZN A 502 1555 1555 2.55 LINK NA NA A 514 O HOH A 628 1555 1555 2.60 LINK NA NA A 514 O HOH A 700 1555 1555 2.60 LINK O LEU B 120 NA NA B 413 1555 1555 2.25 LINK O ILE B 123 NA NA B 413 1555 1555 2.21 LINK OH TYR B 136 NA NA B 413 1555 1555 2.74 LINK SG CYS B 189 ZN ZN B 404 1555 1555 2.38 LINK SG CYS B 192 ZN ZN B 404 1555 1555 2.38 LINK SG CYS B 224 ZN ZN B 404 1555 1555 2.52 LINK SG CYS B 226 ZN ZN B 404 1555 1555 2.45 LINK NA NA B 413 O HOH B 588 1555 1555 2.34 LINK NA NA B 413 O HOH B 592 1555 1555 2.40 CRYST1 114.887 114.887 252.820 90.00 90.00 120.00 P 65 2 2 24 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 0.008704 0.005025 0.000000 0.00000 SCALE2 0.000000 0.010051 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003955 0.00000