HEADER HYDROLASE/INHIBITOR 18-OCT-22 8EUA TITLE STRUCTURE OF SARS-COV2 PLPRO BOUND TO A COVALENT INHIBITOR 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, COVID-19 VIRUS; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: BL21(DE3) KEYWDS PLPRO, SARS-COV2, COVALENT INHIBITOR, HYDROLASE, HYDROLASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.I.MATHEWS,S.POKHREL,S.WAKATSUKI REVDAT 2 25-OCT-23 8EUA 1 REMARK REVDAT 1 05-APR-23 8EUA 0 JRNL AUTH B.C.SANDERS,S.POKHREL,A.D.LABBE,I.I.MATHEWS,C.J.COOPER, JRNL AUTH 2 R.B.DAVIDSON,G.PHILLIPS,K.L.WEISS,Q.ZHANG,H.O'NEILL,M.KAUR, JRNL AUTH 3 J.G.SCHMIDT,W.REICHARD,S.SURENDRANATHAN,J.PARVATHAREDDY, JRNL AUTH 4 L.PHILLIPS,C.RAINVILLE,D.E.STERNER,D.KUMARAN,B.ANDI, JRNL AUTH 5 G.BABNIGG,N.W.MORIARTY,P.D.ADAMS,A.JOACHIMIAK,B.L.HURST, JRNL AUTH 6 S.KUMAR,T.R.BUTT,C.B.JONSSON,L.FERRINS,S.WAKATSUKI, JRNL AUTH 7 S.GALANIE,M.S.HEAD,J.M.PARKS JRNL TITL POTENT AND SELECTIVE COVALENT INHIBITION OF THE PAPAIN-LIKE JRNL TITL 2 PROTEASE FROM SARS-COV-2. JRNL REF NAT COMMUN V. 14 1733 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36977673 JRNL DOI 10.1038/S41467-023-37254-W REMARK 2 REMARK 2 RESOLUTION. 3.10 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12359 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) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 651 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) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 872 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.4080 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 41 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 85.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 90.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.50000 REMARK 3 B22 (A**2) : 2.50000 REMARK 3 B33 (A**2) : -5.01000 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): 0.658 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.363 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.279 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.092 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.869 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2575 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2348 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3491 ; 1.786 ; 1.680 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5419 ; 1.220 ; 1.592 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 310 ; 8.640 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;42.662 ;23.884 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 427 ;21.165 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;14.094 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 336 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2904 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 592 ; 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 : NULL 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 : REFINED INDIVIDUALLY REMARK 4 REMARK 4 8EUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269273. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUL-21 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 : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : RH COATED COLLIMATING MIRRORS, K REMARK 200 -B FOCUSING MIRRORS 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 : 13010 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 25.66 REMARK 200 R MERGE (I) : 0.43600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 24.49 REMARK 200 R MERGE FOR SHELL (I) : 7.05000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 6WX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CACL2, CDCL2 AND COCL3, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 56.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 56.16500 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 108.66500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.33250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 56.16500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 162.99750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 162.99750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.16500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 54.33250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 56.16500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 108.66500 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 56.16500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 56.16500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 108.66500 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 56.16500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 162.99750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 54.33250 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 56.16500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 54.33250 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 162.99750 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 56.16500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 56.16500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 108.66500 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 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 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 A 531 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 541 LIES ON A SPECIAL POSITION. 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 A -1 REMARK 465 ARG A 0 REMARK 465 GLU A 1 REMARK 465 VAL A 2 REMARK 465 ILE A 314 REMARK 465 LYS A 315 REMARK 465 PRO A 316 REMARK 465 LEU A 317 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 CYS A 270 O HOH A 501 1.99 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 OE1 GLN A 195 O CYS A 226 8555 2.11 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 CYS A 189 CA - CB - SG ANGL. DEV. = 12.8 DEGREES REMARK 500 CYS A 224 CA - CB - SG ANGL. DEV. = -12.1 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 PHE A 31 -66.54 -109.27 REMARK 500 PRO A 46 109.36 -42.99 REMARK 500 ASN A 60 -68.35 -93.85 REMARK 500 ASP A 61 139.30 -38.08 REMARK 500 HIS A 73 29.10 44.60 REMARK 500 ASN A 99 43.60 71.22 REMARK 500 ASP A 108 43.18 24.22 REMARK 500 THR A 225 -76.24 -53.22 REMARK 500 LYS A 228 -97.98 -116.18 REMARK 500 VAL A 235 -79.76 -68.68 REMARK 500 PRO A 248 107.26 -49.46 REMARK 500 TYR A 268 105.52 -34.33 REMARK 500 GLN A 269 7.61 81.28 REMARK 500 CYS A 270 46.17 -143.39 REMARK 500 LYS A 279 -129.73 -91.19 REMARK 500 SER A 293 140.92 177.90 REMARK 500 ASN A 308 -45.84 -152.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE A 222 PRO A 223 144.35 REMARK 500 LYS A 228 GLN A 229 -146.22 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 404 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 62 OD1 REMARK 620 2 ASP A 62 OD2 58.4 REMARK 620 3 HIS A 73 ND1 102.0 84.6 REMARK 620 4 HOH A 503 O 107.8 93.8 9.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 108 OD1 REMARK 620 2 ASP A 108 OD2 54.3 REMARK 620 3 CYS A 270 SG 35.9 63.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 189 SG REMARK 620 2 CYS A 192 SG 139.2 REMARK 620 3 CYS A 224 SG 93.7 122.0 REMARK 620 4 CYS A 226 SG 109.9 74.0 115.8 REMARK 620 N 1 2 3 DBREF 8EUA A 0 316 UNP P0DTD1 R1AB_SARS2 1563 1879 SEQADV 8EUA MET A -1 UNP P0DTD1 INITIATING METHIONINE SEQADV 8EUA LEU A 317 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 319 MET ARG GLU VAL ARG THR ILE LYS VAL PHE THR THR VAL SEQRES 2 A 319 ASP ASN ILE ASN LEU HIS THR GLN VAL VAL ASP MET SER SEQRES 3 A 319 MET THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP SEQRES 4 A 319 GLY ALA ASP VAL THR LYS ILE LYS PRO HIS ASN SER HIS SEQRES 5 A 319 GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ASP ASP THR SEQRES 6 A 319 LEU ARG VAL GLU ALA PHE GLU TYR TYR HIS THR THR ASP SEQRES 7 A 319 PRO SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS SEQRES 8 A 319 THR LYS LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU THR SEQRES 9 A 319 SER ILE LYS TRP ALA ASP ASN ASN CYS TYR LEU ALA THR SEQRES 10 A 319 ALA LEU LEU THR LEU GLN GLN ILE GLU LEU LYS PHE ASN SEQRES 11 A 319 PRO PRO ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG ALA SEQRES 12 A 319 GLY GLU ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR SEQRES 13 A 319 CYS ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU SEQRES 14 A 319 THR MET SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SER SEQRES 15 A 319 CYS LYS ARG VAL LEU ASN VAL VAL CYS LYS THR CYS GLY SEQRES 16 A 319 GLN GLN GLN THR THR LEU LYS GLY VAL GLU ALA VAL MET SEQRES 17 A 319 TYR MET GLY THR LEU SER TYR GLU GLN PHE LYS LYS GLY SEQRES 18 A 319 VAL GLN ILE PRO CYS THR CYS GLY LYS GLN ALA THR LYS SEQRES 19 A 319 TYR LEU VAL GLN GLN GLU SER PRO PHE VAL MET MET SER SEQRES 20 A 319 ALA PRO PRO ALA GLN TYR GLU LEU LYS HIS GLY THR PHE SEQRES 21 A 319 THR CYS ALA SER GLU TYR THR GLY ASN TYR GLN CYS GLY SEQRES 22 A 319 HIS TYR LYS HIS ILE THR SER LYS GLU THR LEU TYR CYS SEQRES 23 A 319 ILE ASP GLY ALA LEU LEU THR LYS SER SER GLU TYR LYS SEQRES 24 A 319 GLY PRO ILE THR ASP VAL PHE TYR LYS GLU ASN SER TYR SEQRES 25 A 319 THR THR THR ILE LYS PRO LEU HET WUK A 401 35 HET ZN A 402 1 HET ZN A 403 1 HET ZN A 404 1 HET SO4 A 405 5 HETNAM WUK METHYL 4-{2-[3-(2-{[(1R)-1-(NAPHTHALEN-1-YL) HETNAM 2 WUK ETHYL]CARBAMOYL}PHENYL)PROPANOYL]HYDRAZINYL}-4- HETNAM 3 WUK OXOBUTANOATE HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 WUK C27 H29 N3 O5 FORMUL 3 ZN 3(ZN 2+) FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *41(H2 O) HELIX 1 AA1 THR A 26 PHE A 31 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 LEU A 120 1 11 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 VAL A 57 N THR A 10 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 3 GLY A 193 GLN A 195 0 SHEET 2 AA2 3 LYS A 182 CYS A 189 -1 N VAL A 187 O GLN A 195 SHEET 3 AA2 3 THR A 198 LYS A 200 -1 O LEU A 199 N ARG A 183 SHEET 1 AA3 4 GLY A 193 GLN A 195 0 SHEET 2 AA3 4 LYS A 182 CYS A 189 -1 N VAL A 187 O GLN A 195 SHEET 3 AA3 4 GLN A 229 GLU A 238 -1 O GLU A 238 N LYS A 182 SHEET 4 AA3 4 VAL A 220 PRO A 223 -1 N VAL A 220 O LYS A 232 SHEET 1 AA4 7 MET A 206 MET A 208 0 SHEET 2 AA4 7 PHE A 241 LYS A 254 1 O SER A 245 N TYR A 207 SHEET 3 AA4 7 GLU A 295 LYS A 306 -1 O TYR A 296 N LEU A 253 SHEET 4 AA4 7 CYS A 260 THR A 265 -1 N CYS A 260 O PHE A 304 SHEET 5 AA4 7 HIS A 272 SER A 278 -1 O LYS A 274 N GLU A 263 SHEET 6 AA4 7 LEU A 282 ASP A 286 -1 O ILE A 285 N HIS A 275 SHEET 7 AA4 7 LEU A 289 SER A 293 -1 O THR A 291 N CYS A 284 LINK SG CYS A 111 C1 WUK A 401 1555 1555 1.87 LINK OD1 ASP A 62 ZN ZN A 404 1555 10555 2.29 LINK OD2 ASP A 62 ZN ZN A 404 1555 10555 2.33 LINK ND1 HIS A 73 ZN ZN A 404 1555 1555 2.00 LINK OD1 ASP A 108 ZN ZN A 403 1555 15555 2.30 LINK OD2 ASP A 108 ZN ZN A 403 1555 15555 2.46 LINK SG CYS A 189 ZN ZN A 402 1555 1555 2.40 LINK SG CYS A 192 ZN ZN A 402 1555 1555 2.32 LINK SG CYS A 224 ZN ZN A 402 1555 1555 2.31 LINK SG CYS A 226 ZN ZN A 402 1555 1555 2.36 LINK SG CYS A 270 ZN ZN A 403 1555 1555 2.26 LINK ZN ZN A 404 O HOH A 503 1555 10555 2.23 CRYST1 112.330 112.330 217.330 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 0.008902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004601 0.00000