HEADER HYDROLASE/HYDROLASE INHIBITOR 23-JUL-20 7JIT TITLE THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 , C111S TITLE 2 MUTANT, IN COMPLEX WITH PLP_SNYDER495 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3,PL2-PRO,PAPAIN-LIKE COMPND 5 PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: 3 N-TERMINAL RESIDUES (SNA) ARE FROM 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 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, KEYWDS 3 HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.OSIPIUK,C.TESAR,M.ENDRES,V.LISNYAK,S.MAKI,C.TAYLOR,Y.ZHANG,Z.ZHOU, AUTHOR 2 S.A.AZIZI,K.JONES,R.KATHAYAT,S.A.SNYDER,B.C.DICKINSON,A.JOACHIMIAK, AUTHOR 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) REVDAT 5 18-OCT-23 7JIT 1 REMARK REVDAT 4 31-MAR-21 7JIT 1 HEADER TITLE COMPND KEYWDS REVDAT 3 10-FEB-21 7JIT 1 JRNL REVDAT 2 27-JAN-21 7JIT 1 COMPND REVDAT 1 05-AUG-20 7JIT 0 JRNL AUTH J.OSIPIUK,S.A.AZIZI,S.DVORKIN,M.ENDRES,R.JEDRZEJCZAK, JRNL AUTH 2 K.A.JONES,S.KANG,R.S.KATHAYAT,Y.KIM,V.G.LISNYAK,S.L.MAKI, JRNL AUTH 3 V.NICOLAESCU,C.A.TAYLOR,C.TESAR,Y.A.ZHANG,Z.ZHOU,G.RANDALL, JRNL AUTH 4 K.MICHALSKA,S.A.SNYDER,B.C.DICKINSON,A.JOACHIMIAK JRNL TITL STRUCTURE OF PAPAIN-LIKE PROTEASE FROM SARS-COV-2 AND ITS JRNL TITL 2 COMPLEXES WITH NON-COVALENT INHIBITORS. JRNL REF NAT COMMUN V. 12 743 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33531496 JRNL DOI 10.1038/S41467-021-21060-3 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 49570 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2620 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2493 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.12000 REMARK 3 B22 (A**2) : 1.12000 REMARK 3 B33 (A**2) : -2.24000 REMARK 3 B12 (A**2) : 0.00000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.999 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2682 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2412 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3655 ; 1.677 ; 1.674 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5637 ; 1.366 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 337 ; 6.201 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;39.702 ;23.740 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 458 ;14.495 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.588 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3010 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 562 ; 0.007 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 315 REMARK 3 RESIDUE RANGE : A 501 A 511 REMARK 3 ORIGIN FOR THE GROUP (A): 49.413 37.787 14.493 REMARK 3 T TENSOR REMARK 3 T11: 0.0517 T22: 0.0601 REMARK 3 T33: 0.0455 T12: 0.0121 REMARK 3 T13: 0.0062 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.6517 L22: 1.3386 REMARK 3 L33: 0.9287 L12: -0.3385 REMARK 3 L13: -0.0834 L23: 0.0181 REMARK 3 S TENSOR REMARK 3 S11: 0.0612 S12: -0.0124 S13: 0.0812 REMARK 3 S21: -0.0512 S22: -0.1598 S23: -0.0786 REMARK 3 S31: 0.0387 S32: 0.0517 S33: 0.0986 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 7JIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1000250862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52219 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 49.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 16.60 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.9000 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) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 1.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 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: 6WZU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES BUFFER, 0.2 M ZINC ACETATE, REMARK 280 10% PEG 8000, 4 MM PLP_SNYDER495, PH 6.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+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 56.95650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 56.95650 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 109.66400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.83200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.95650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 164.49600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 164.49600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.95650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.83200 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 56.95650 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 109.66400 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 56.95650 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 109.66400 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 56.95650 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 164.49600 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 54.83200 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 56.95650 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 54.83200 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 164.49600 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 56.95650 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 56.95650 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 109.66400 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 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 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 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 601 O HOH A 606 1.38 REMARK 500 O HOH A 725 O HOH A 741 1.70 REMARK 500 O HOH A 601 O HOH A 777 1.77 REMARK 500 O HOH A 725 O HOH A 794 1.80 REMARK 500 O HOH A 604 O HOH A 608 1.96 REMARK 500 O HOH A 604 O HOH A 687 1.96 REMARK 500 O HOH A 723 O HOH A 750 1.97 REMARK 500 O HOH A 604 O HOH A 738 2.00 REMARK 500 O HOH A 606 O HOH A 741 2.03 REMARK 500 O HOH A 608 O HOH A 687 2.06 REMARK 500 ND1 HIS A 255 O HOH A 601 2.17 REMARK 500 O HOH A 604 O HOH A 820 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 136 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES 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 ILE A 14 -54.76 -124.52 REMARK 500 TYR A 95 73.42 -119.29 REMARK 500 SER A 103 -168.93 -104.01 REMARK 500 GLU A 143 79.20 -113.16 REMARK 500 THR A 191 -64.40 -90.88 REMARK 500 GLN A 269 -43.85 77.18 REMARK 500 LYS A 279 -132.06 -113.10 REMARK 500 ASN A 308 -65.85 -139.45 REMARK 500 ASN A 308 -74.05 -135.01 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 A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 GLU A 67 OE2 141.6 REMARK 620 3 HOH A 788 O 101.6 97.8 REMARK 620 4 HOH A 789 O 102.4 108.1 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 HIS A 73 ND1 114.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 ASP A 108 OD2 120.1 REMARK 620 3 CYS A 270 SG 115.5 40.1 REMARK 620 4 HOH A 744 O 111.5 86.6 121.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 ND1 REMARK 620 2 CYS A 270 SG 71.6 REMARK 620 3 HOH A 744 O 100.9 75.7 REMARK 620 N 1 2 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 135.6 REMARK 620 3 CYS A 224 SG 105.9 107.0 REMARK 620 4 CYS A 226 SG 88.6 115.5 97.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES 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: 6WZU RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 REMARK 900 RELATED ID: 7JIR RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF PAPAIN-LIKE PROTEASE OF SARS COV-2 , C111S REMARK 900 MUTANT, IN COMPLEX WITH PLP_SNYDER457 DBREF 7JIT A 1 315 UNP P0DTC1 R1A_SARS2 1564 1878 SEQADV 7JIT SER A -2 UNP P0DTC1 EXPRESSION TAG SEQADV 7JIT ASN A -1 UNP P0DTC1 EXPRESSION TAG SEQADV 7JIT ALA A 0 UNP P0DTC1 EXPRESSION TAG SEQADV 7JIT SER A 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 HET Y95 A 501 29 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 2 HET ZN A 505 1 HET CL A 506 1 HET CL A 507 1 HET CL A 508 1 HET MES A 509 12 HET ACT A 510 4 HET ACT A 511 4 HETNAM Y95 5-[(CARBAMOYLCARBAMOYL)AMINO]-2-METHYL-N-[(1R)-1- HETNAM 2 Y95 (NAPHTHALEN-1-YL)ETHYL]BENZAMIDE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM ACT ACETATE ION FORMUL 2 Y95 C22 H22 N4 O3 FORMUL 3 ZN 4(ZN 2+) FORMUL 7 CL 3(CL 1-) FORMUL 10 MES C6 H13 N O4 S FORMUL 11 ACT 2(C2 H3 O2 1-) FORMUL 13 HOH *230(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 ASN A 156 1 13 HELIX 8 AA8 ASP A 164 GLN A 174 1 11 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 ILE A 5 O VAL A 21 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 CYS A 189 O GLY A 193 SHEET 3 AA3 4 GLN A 229 GLU A 238 -1 O GLN A 236 N VAL A 184 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 CYS A 189 O GLY A 193 SHEET 3 AA4 4 GLN A 229 GLU A 238 -1 O GLN A 236 N VAL A 184 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 LEU A 253 1 O SER A 245 N TYR A 207 SHEET 3 AA5 7 TYR A 296 LYS A 306 -1 O VAL A 303 N MET A 244 SHEET 4 AA5 7 CYS A 260 THR A 265 -1 N CYS A 260 O PHE A 304 SHEET 5 AA5 7 HIS A 272 SER A 278 -1 O ILE A 276 N ALA A 261 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 LINK NE2 HIS A 17 ZN ZN A 503 1555 1555 1.96 LINK OD1 ASP A 62 ZN ZN A 505 1555 10665 1.95 LINK OE2 GLU A 67 ZN ZN A 503 1555 1555 2.17 LINK ND1 HIS A 73 ZN ZN A 505 1555 1555 1.98 LINK ND1 HIS A 89 ZN A ZN A 504 1555 1555 2.11 LINK ND1 HIS A 89 ZN B ZN A 504 1555 1555 2.11 LINK OD2 ASP A 108 ZN A ZN A 504 1555 1555 2.18 LINK SG CYS A 189 ZN ZN A 502 1555 1555 2.55 LINK SG CYS A 192 ZN ZN A 502 1555 1555 2.40 LINK SG CYS A 224 ZN ZN A 502 1555 1555 2.25 LINK SG CYS A 226 ZN ZN A 502 1555 1555 2.69 LINK SG CYS A 270 ZN A ZN A 504 1555 15555 2.56 LINK SG CYS A 270 ZN B ZN A 504 1555 15555 2.31 LINK ZN ZN A 503 O HOH A 788 1555 1555 2.13 LINK ZN ZN A 503 O HOH A 789 1555 1555 2.12 LINK ZN A ZN A 504 O HOH A 744 1555 1555 2.00 LINK ZN B ZN A 504 O HOH A 744 1555 1555 2.30 CRYST1 113.913 113.913 219.328 90.00 90.00 90.00 I 41 2 2 16 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 0.008779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004559 0.00000