HEADER HYDROLASE/HYDROLASE INHIBITOR 09-MAY-20 6WX4
TITLE CRYSTAL STRUCTURE OF THE SARS COV-2 PAPAIN-LIKE PROTEASE IN COMPLEX
TITLE 2 WITH PEPTIDE INHIBITOR VIR251
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3;
COMPND 3 CHAIN: D;
COMPND 4 SYNONYM: PAPAIN-LIKE PROTEASE,PP1AB,ORF1AB POLYPROTEIN,NSP3,PL2-PRO,
COMPND 5 PAPAIN-LIKE PROTEINASE,PL-PRO;
COMPND 6 EC: 3.4.19.121, 3.4.22.-;
COMPND 7 ENGINEERED: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: VIR251;
COMPND 10 CHAIN: I;
COMPND 11 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS
SOURCE 3 2;
SOURCE 4 ORGANISM_COMMON: 2019-NCOV;
SOURCE 5 ORGANISM_TAXID: 2697049;
SOURCE 6 GENE: REP, 1A-1B;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: CODON PLUS;
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET29B;
SOURCE 12 MOL_ID: 2;
SOURCE 13 SYNTHETIC: YES;
SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 15 ORGANISM_TAXID: 32360
KEYWDS COVID-19, CORONAVIRUS, SARS, COV-2, PAPAIN-LIKE PROTEASE, PLPRO,
KEYWDS 2 DEUBIQUITINATING ENZYME, UBIQUITIN, ACTIVITY-BASED PROBE, HYDROLASE-
KEYWDS 3 HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Z.LV,S.K.OLSEN
REVDAT 6 15-NOV-23 6WX4 1 LINK ATOM
REVDAT 5 18-OCT-23 6WX4 1 JRNL
REVDAT 4 27-JAN-21 6WX4 1 COMPND
REVDAT 3 02-DEC-20 6WX4 1 JRNL
REVDAT 2 24-JUN-20 6WX4 1 JRNL
REVDAT 1 20-MAY-20 6WX4 0
JRNL AUTH W.RUT,Z.LV,M.ZMUDZINSKI,S.PATCHETT,D.NAYAK,S.J.SNIPAS,
JRNL AUTH 2 F.EL OUALID,T.T.HUANG,M.BEKES,M.DRAG,S.K.OLSEN
JRNL TITL ACTIVITY PROFILING AND CRYSTAL STRUCTURES OF INHIBITOR-BOUND
JRNL TITL 2 SARS-COV-2 PAPAIN-LIKE PROTEASE: A FRAMEWORK FOR
JRNL TITL 3 ANTI-COVID-19 DRUG DESIGN.
JRNL REF SCI ADV V. 6 2020
JRNL REFN ESSN 2375-2548
JRNL PMID 33067239
JRNL DOI 10.1126/SCIADV.ABD4596
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH W.RUT,Z.LV,M.ZMUDZINSKI,S.PATCHETT,D.NAYAK,S.J.SNIPAS,
REMARK 1 AUTH 2 F.EL OUALID,T.T.HUANG,M.BEKES,M.DRAG,S.K.OLSEN
REMARK 1 TITL ACTIVITY PROFILING AND STRUCTURES OF INHIBITOR-BOUND
REMARK 1 TITL 2 SARS-COV-2-PLPRO PROTEASE PROVIDES A FRAMEWORK FOR
REMARK 1 TITL 3 ANTI-COVID-19 DRUG DESIGN.
REMARK 1 REF BIORXIV 2020
REMARK 1 REFN ISSN 2692-8205
REMARK 1 PMID 32511411
REMARK 1 DOI 10.1101/2020.04.29.068890
REMARK 2
REMARK 2 RESOLUTION. 1.66 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.10_2155
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.73
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 46301
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.171
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : 0.196
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.320
REMARK 3 FREE R VALUE TEST SET COUNT : 2000
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 90.7000 - 3.9889 1.00 3373 153 0.1554 0.1829
REMARK 3 2 3.9889 - 3.1660 1.00 3243 145 0.1579 0.1831
REMARK 3 3 3.1660 - 2.7658 1.00 3190 145 0.1834 0.1932
REMARK 3 4 2.7658 - 2.5129 1.00 3197 145 0.1885 0.2150
REMARK 3 5 2.5129 - 2.3328 1.00 3178 143 0.1793 0.2070
REMARK 3 6 2.3328 - 2.1952 1.00 3169 143 0.1714 0.2268
REMARK 3 7 2.1952 - 2.0853 1.00 3169 143 0.1645 0.1771
REMARK 3 8 2.0853 - 1.9945 1.00 3137 142 0.1593 0.1753
REMARK 3 9 1.9945 - 1.9177 1.00 3164 142 0.1637 0.2134
REMARK 3 10 1.9177 - 1.8515 1.00 3123 141 0.1809 0.2294
REMARK 3 11 1.8515 - 1.7936 1.00 3115 141 0.1950 0.2186
REMARK 3 12 1.7936 - 1.7424 1.00 3165 143 0.2001 0.2303
REMARK 3 13 1.7424 - 1.6965 1.00 3145 141 0.2164 0.2149
REMARK 3 14 1.6965 - 1.6551 0.94 2933 133 0.2407 0.2575
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.050
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 28.43
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.69
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.006 2646
REMARK 3 ANGLE : 0.844 3581
REMARK 3 CHIRALITY : 0.049 394
REMARK 3 PLANARITY : 0.005 457
REMARK 3 DIHEDRAL : 11.852 1557
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'D' AND (RESID 1 THROUGH 78 )
REMARK 3 ORIGIN FOR THE GROUP (A): -13.8584 -11.2780 -14.0916
REMARK 3 T TENSOR
REMARK 3 T11: 0.3251 T22: 0.3506
REMARK 3 T33: 0.3134 T12: 0.0123
REMARK 3 T13: 0.0177 T23: -0.0422
REMARK 3 L TENSOR
REMARK 3 L11: 0.5245 L22: 0.1438
REMARK 3 L33: 2.2132 L12: -0.1752
REMARK 3 L13: -1.0808 L23: -0.4358
REMARK 3 S TENSOR
REMARK 3 S11: -0.0851 S12: -0.1137 S13: 0.0327
REMARK 3 S21: 0.1576 S22: -0.1168 S23: 0.2863
REMARK 3 S31: -0.1612 S32: -0.1082 S33: -0.0021
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'D' AND (RESID 79 THROUGH 175 )
REMARK 3 ORIGIN FOR THE GROUP (A): 1.4659 -13.7040 -32.6477
REMARK 3 T TENSOR
REMARK 3 T11: 0.1988 T22: 0.1949
REMARK 3 T33: 0.2373 T12: 0.0074
REMARK 3 T13: -0.0303 T23: -0.0115
REMARK 3 L TENSOR
REMARK 3 L11: 1.5677 L22: 1.2118
REMARK 3 L33: 1.7672 L12: -0.2905
REMARK 3 L13: -0.8826 L23: 0.2411
REMARK 3 S TENSOR
REMARK 3 S11: 0.0298 S12: -0.0705 S13: 0.0893
REMARK 3 S21: -0.0451 S22: -0.0103 S23: -0.0354
REMARK 3 S31: -0.0252 S32: 0.0209 S33: -0.0000
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'D' AND (RESID 176 THROUGH 228 )
REMARK 3 ORIGIN FOR THE GROUP (A): -2.9160 -22.8573 -59.9614
REMARK 3 T TENSOR
REMARK 3 T11: 0.3779 T22: 0.3633
REMARK 3 T33: 0.2936 T12: 0.0183
REMARK 3 T13: -0.0564 T23: -0.0535
REMARK 3 L TENSOR
REMARK 3 L11: 0.5902 L22: 0.6141
REMARK 3 L33: 0.7739 L12: 0.0199
REMARK 3 L13: 0.2977 L23: 0.0719
REMARK 3 S TENSOR
REMARK 3 S11: -0.0727 S12: 0.0717 S13: -0.2218
REMARK 3 S21: -0.1561 S22: -0.0584 S23: 0.0870
REMARK 3 S31: -0.0391 S32: -0.2431 S33: -0.0083
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'D' AND (RESID 229 THROUGH 320 )
REMARK 3 ORIGIN FOR THE GROUP (A): 9.5523 -17.2123 -51.7144
REMARK 3 T TENSOR
REMARK 3 T11: 0.3161 T22: 0.2369
REMARK 3 T33: 0.2731 T12: -0.0152
REMARK 3 T13: 0.0007 T23: 0.0181
REMARK 3 L TENSOR
REMARK 3 L11: 0.8389 L22: 0.3820
REMARK 3 L33: 2.2939 L12: -0.0417
REMARK 3 L13: 0.5363 L23: 0.9524
REMARK 3 S TENSOR
REMARK 3 S11: -0.0867 S12: 0.0479 S13: 0.0794
REMARK 3 S21: -0.2464 S22: 0.0053 S23: -0.2079
REMARK 3 S31: -0.3203 S32: 0.1483 S33: -0.0055
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 6WX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-20.
REMARK 100 THE DEPOSITION ID IS D_1000249136.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-MAY-20
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46470
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650
REMARK 200 RESOLUTION RANGE LOW (A) : 90.730
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 13.20
REMARK 200 R MERGE (I) : 0.09400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68
REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0
REMARK 200 DATA REDUNDANCY IN SHELL : 11.50
REMARK 200 R MERGE FOR SHELL (I) : 1.73200
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 6WUU
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.88
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M POTASSIUM SODIUM TARTRATE
REMARK 280 TETRAHYDRATE, 0.1 M TRIS HCL PH 8.5 AND 0.5% W/V POLYETHYLENE
REMARK 280 GLYCOL MONOMETHYL ETHER 5,000, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 22.43450
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.74100
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.52400
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 22.43450
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.74100
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.52400
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 22.43450
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.74100
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 75.52400
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 22.43450
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.74100
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.52400
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, I
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH D 615 LIES ON A SPECIAL POSITION.
REMARK 375 HOH D 752 LIES ON A SPECIAL POSITION.
REMARK 400
REMARK 400 COMPOUND
REMARK 400 PEPTIDE COVALENTLY LINKED TO ACTIVE SITE CYS
REMARK 400
REMARK 400 THE VIR251PAPAIN-LIKE PROTEASE PEPTIDE INHIBITOR IS PEPTIDE-LIKE, A
REMARK 400 MEMBER OF ENZYME INHIBITOR CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: VIR251PAPAIN-LIKE PROTEASE PEPTIDE INHIBITOR
REMARK 400 CHAIN: I
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET D -1
REMARK 465 ARG D 0
REMARK 465 HIS D 321
REMARK 465 HIS D 322
REMARK 465 HIS D 323
REMARK 465 HIS D 324
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH D 616 O HOH D 767 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 SER D 103 -168.43 -111.82
REMARK 500 GLU D 143 77.63 -106.82
REMARK 500 CYS D 270 85.40 -153.16
REMARK 500 LYS D 279 -126.49 -118.03
REMARK 500 ASN D 308 -66.10 -139.05
REMARK 500 GLU D 318 -175.25 -66.85
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN D 501 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 189 SG
REMARK 620 2 CYS D 192 SG 106.4
REMARK 620 3 CYS D 224 SG 108.3 116.2
REMARK 620 4 CYS D 226 SG 115.9 109.8 100.5
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues ACY A 1 and 73O A 2
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residues 73O A 2 and DPP A 3
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 6WUU RELATED DB: PDB
REMARK 900 THIS IS THE SAME ENZYME IN COMPLEX WITH A DIFFERENT INHIBITOR. I
REMARK 900 WOULD LIKE TO RELEASE THESE COORDINATES TOGETHER AND I CAN CHANGE
REMARK 900 TO RELEASE IMMEDIATELY AS LONG AS THEY RELEASE TOGETHER.
DBREF 6WX4 D 0 316 UNP P0DTD1 R1AB_SARS2 1563 1879
DBREF 6WX4 I 1 5 PDB 6WX4 6WX4 1 5
SEQADV 6WX4 MET D -1 UNP P0DTD1 INITIATING METHIONINE
SEQADV 6WX4 LEU D 317 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 GLU D 318 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 319 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 320 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 321 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 322 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 323 UNP P0DTD1 EXPRESSION TAG
SEQADV 6WX4 HIS D 324 UNP P0DTD1 EXPRESSION TAG
SEQRES 1 D 326 MET ARG GLU VAL ARG THR ILE LYS VAL PHE THR THR VAL
SEQRES 2 D 326 ASP ASN ILE ASN LEU HIS THR GLN VAL VAL ASP MET SER
SEQRES 3 D 326 MET THR TYR GLY GLN GLN PHE GLY PRO THR TYR LEU ASP
SEQRES 4 D 326 GLY ALA ASP VAL THR LYS ILE LYS PRO HIS ASN SER HIS
SEQRES 5 D 326 GLU GLY LYS THR PHE TYR VAL LEU PRO ASN ASP ASP THR
SEQRES 6 D 326 LEU ARG VAL GLU ALA PHE GLU TYR TYR HIS THR THR ASP
SEQRES 7 D 326 PRO SER PHE LEU GLY ARG TYR MET SER ALA LEU ASN HIS
SEQRES 8 D 326 THR LYS LYS TRP LYS TYR PRO GLN VAL ASN GLY LEU THR
SEQRES 9 D 326 SER ILE LYS TRP ALA ASP ASN ASN CYS TYR LEU ALA THR
SEQRES 10 D 326 ALA LEU LEU THR LEU GLN GLN ILE GLU LEU LYS PHE ASN
SEQRES 11 D 326 PRO PRO ALA LEU GLN ASP ALA TYR TYR ARG ALA ARG ALA
SEQRES 12 D 326 GLY GLU ALA ALA ASN PHE CYS ALA LEU ILE LEU ALA TYR
SEQRES 13 D 326 CYS ASN LYS THR VAL GLY GLU LEU GLY ASP VAL ARG GLU
SEQRES 14 D 326 THR MET SER TYR LEU PHE GLN HIS ALA ASN LEU ASP SER
SEQRES 15 D 326 CYS LYS ARG VAL LEU ASN VAL VAL CYS LYS THR CYS GLY
SEQRES 16 D 326 GLN GLN GLN THR THR LEU LYS GLY VAL GLU ALA VAL MET
SEQRES 17 D 326 TYR MET GLY THR LEU SER TYR GLU GLN PHE LYS LYS GLY
SEQRES 18 D 326 VAL GLN ILE PRO CYS THR CYS GLY LYS GLN ALA THR LYS
SEQRES 19 D 326 TYR LEU VAL GLN GLN GLU SER PRO PHE VAL MET MET SER
SEQRES 20 D 326 ALA PRO PRO ALA GLN TYR GLU LEU LYS HIS GLY THR PHE
SEQRES 21 D 326 THR CYS ALA SER GLU TYR THR GLY ASN TYR GLN CYS GLY
SEQRES 22 D 326 HIS TYR LYS HIS ILE THR SER LYS GLU THR LEU TYR CYS
SEQRES 23 D 326 ILE ASP GLY ALA LEU LEU THR LYS SER SER GLU TYR LYS
SEQRES 24 D 326 GLY PRO ILE THR ASP VAL PHE TYR LYS GLU ASN SER TYR
SEQRES 25 D 326 THR THR THR ILE LYS PRO LEU GLU HIS HIS HIS HIS HIS
SEQRES 26 D 326 HIS
SEQRES 1 I 5 ACY 73O DPP GLY GVE
HET ACY I 1 3
HET 73O I 2 13
HET DPP I 3 6
HET GVE I 5 8
HET ZN D 501 1
HETNAM ACY ACETIC ACID
HETNAM 73O (2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID
HETNAM DPP DIAMINOPROPANOIC ACID
HETNAM GVE METHYL 4-AMINOBUTANOATE
HETNAM ZN ZINC ION
FORMUL 2 ACY C2 H4 O2
FORMUL 2 73O C10 H13 N O3
FORMUL 2 DPP C3 H8 N2 O2
FORMUL 2 GVE C5 H11 N O2
FORMUL 3 ZN ZN 2+
FORMUL 4 HOH *194(H2 O)
HELIX 1 AA1 THR D 26 GLY D 32 1 7
HELIX 2 AA2 HIS D 47 GLU D 51 5 5
HELIX 3 AA3 ASP D 61 HIS D 73 1 13
HELIX 4 AA4 SER D 78 LYS D 91 1 14
HELIX 5 AA5 ASN D 110 GLN D 121 1 12
HELIX 6 AA6 PRO D 129 ALA D 141 1 13
HELIX 7 AA7 ALA D 144 ASN D 156 1 13
HELIX 8 AA8 ASP D 164 GLN D 174 1 11
HELIX 9 AA9 GLY D 201 VAL D 205 1 5
HELIX 10 AB1 SER D 212 GLY D 219 1 8
SHEET 1 AA1 5 HIS D 17 ASP D 22 0
SHEET 2 AA1 5 THR D 4 THR D 10 -1 N VAL D 7 O GLN D 19
SHEET 3 AA1 5 THR D 54 VAL D 57 1 O PHE D 55 N PHE D 8
SHEET 4 AA1 5 THR D 34 LEU D 36 -1 N TYR D 35 O TYR D 56
SHEET 5 AA1 5 ALA D 39 ASP D 40 -1 O ALA D 39 N LEU D 36
SHEET 1 AA2 2 GLN D 97 VAL D 98 0
SHEET 2 AA2 2 LEU D 101 THR D 102 -1 O LEU D 101 N VAL D 98
SHEET 1 AA3 4 GLY D 193 LYS D 200 0
SHEET 2 AA3 4 LYS D 182 CYS D 189 -1 N ARG D 183 O LEU D 199
SHEET 3 AA3 4 GLN D 229 GLU D 238 -1 O THR D 231 N VAL D 188
SHEET 4 AA3 4 VAL D 220 PRO D 223 -1 N ILE D 222 O ALA D 230
SHEET 1 AA4 4 GLY D 193 LYS D 200 0
SHEET 2 AA4 4 LYS D 182 CYS D 189 -1 N ARG D 183 O LEU D 199
SHEET 3 AA4 4 GLN D 229 GLU D 238 -1 O THR D 231 N VAL D 188
SHEET 4 AA4 4 SER D 309 THR D 311 -1 O TYR D 310 N GLN D 237
SHEET 1 AA5 7 MET D 206 MET D 208 0
SHEET 2 AA5 7 PHE D 241 LEU D 253 1 O SER D 245 N TYR D 207
SHEET 3 AA5 7 TYR D 296 LYS D 306 -1 O VAL D 303 N MET D 244
SHEET 4 AA5 7 CYS D 260 ASN D 267 -1 N CYS D 260 O PHE D 304
SHEET 5 AA5 7 CYS D 270 SER D 278 -1 O ILE D 276 N ALA D 261
SHEET 6 AA5 7 LEU D 282 ASP D 286 -1 O ILE D 285 N HIS D 275
SHEET 7 AA5 7 LEU D 289 SER D 293 -1 O LEU D 289 N ASP D 286
LINK SG CYS D 111 CB GVE I 5 1555 1555 1.79
LINK C ACY I 1 N 73O I 2 1555 1555 1.45
LINK C 73O I 2 N DPP I 3 1555 1555 1.44
LINK C DPP I 3 N GLY I 4 1555 1555 1.43
LINK C GLY I 4 N GVE I 5 1555 1555 1.44
LINK SG CYS D 189 ZN ZN D 501 1555 1555 2.36
LINK SG CYS D 192 ZN ZN D 501 1555 1555 2.34
LINK SG CYS D 224 ZN ZN D 501 1555 1555 2.40
LINK SG CYS D 226 ZN ZN D 501 1555 1555 2.28
SITE 1 AC1 4 CYS D 189 CYS D 192 CYS D 224 CYS D 226
SITE 1 AC2 13 DPP I 3 HOH I 101 HOH I 102 ASP D 76
SITE 2 AC2 13 ARG D 82 ASN D 156 GLY D 163 ASP D 164
SITE 3 AC2 13 PRO D 248 TYR D 264 TYR D 268 TYR D 273
SITE 4 AC2 13 HOH D 647
SITE 1 AC3 15 ACY I 1 GLY I 4 HOH I 101 ASP D 76
SITE 2 AC3 15 ARG D 82 ASN D 156 GLY D 163 ASP D 164
SITE 3 AC3 15 PRO D 248 TYR D 264 TYR D 268 GLN D 269
SITE 4 AC3 15 GLY D 271 TYR D 273 HOH D 743
CRYST1 44.869 113.482 151.048 90.00 90.00 90.00 I 2 2 2 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.022287 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008812 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006620 0.00000