HEADER HYDROLASE 13-OCT-12 2YNB
TITLE CRYSTAL STRUCTURE OF THE MAIN PROTEASE OF CORONAVIRUS HKU4 IN COMPLEX
TITLE 2 WITH A MICHAEL ACCEPTOR SG85
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 3C-LIKE PROTEINASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: BAT CORONAVIRUS HKU4 MAIN PROTEASE, 3CL-PRO, 3CLP, NSP5;
COMPND 5 EC: 3.4.22.69;
COMPND 6 ENGINEERED: YES;
COMPND 7 OTHER_DETAILS: SG85 IS LINKED TO CYSTEINE 148 OF CHAIN B
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: TYLONYCTERIS BAT CORONAVIRUS HKU4;
SOURCE 3 ORGANISM_TAXID: 694007;
SOURCE 4 STRAIN: HKU4-1;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GOLD
KEYWDS HYDROLASE, SARS, MICHAEL ACCEPTOR
EXPDTA X-RAY DIFFRACTION
AUTHOR Q.MA,Y.XIAO,R.HILGENFELD
REVDAT 4 23-OCT-24 2YNB 1 REMARK LINK
REVDAT 3 15-MAY-19 2YNB 1 REMARK
REVDAT 2 06-MAR-19 2YNB 1 REMARK LINK
REVDAT 1 23-OCT-13 2YNB 0
JRNL AUTH Q.MA,Y.XIAO,R.HILGENFELD
JRNL TITL INHIBITOR FOR THE MAIN PROTEASE OF CORONAVIRUS HKU4
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.96 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.2
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.72
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 47400
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) : 0.173
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.198
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2370
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.01
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.48
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 3233
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1860
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3070
REMARK 3 BIN R VALUE (WORKING SET) : 0.1841
REMARK 3 BIN FREE R VALUE : 0.2217
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.04
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4618
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 49
REMARK 3 SOLVENT ATOMS : 481
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 29.82
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.67
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.80220
REMARK 3 B22 (A**2) : -1.80220
REMARK 3 B33 (A**2) : 3.60450
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.221
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.153
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.130
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.268
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.128
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 9445 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 17027 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 2049 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 111 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 1476 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 9445 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 645 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 10585 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.09
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.93
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.88
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN A
REMARK 3 ORIGIN FOR THE GROUP (A): 17.1313 51.1430 27.1805
REMARK 3 T TENSOR
REMARK 3 T11: -0.0523 T22: -0.0822
REMARK 3 T33: -0.0971 T12: 0.0601
REMARK 3 T13: 0.0004 T23: 0.0209
REMARK 3 L TENSOR
REMARK 3 L11: 1.2154 L22: 0.4683
REMARK 3 L33: 1.0866 L12: 0.0154
REMARK 3 L13: -0.6713 L23: 0.0363
REMARK 3 S TENSOR
REMARK 3 S11: 0.0112 S12: -0.0309 S13: -0.0653
REMARK 3 S21: 0.0769 S22: -0.0387 S23: -0.1023
REMARK 3 S31: 0.0128 S32: 0.0835 S33: 0.0275
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN B
REMARK 3 ORIGIN FOR THE GROUP (A): -3.9636 42.1809 14.9869
REMARK 3 T TENSOR
REMARK 3 T11: -0.1144 T22: -0.0251
REMARK 3 T33: -0.0791 T12: 0.0325
REMARK 3 T13: 0.0197 T23: -0.0207
REMARK 3 L TENSOR
REMARK 3 L11: 1.5779 L22: 1.3627
REMARK 3 L33: 1.0586 L12: -0.8129
REMARK 3 L13: 0.5126 L23: -0.3034
REMARK 3 S TENSOR
REMARK 3 S11: -0.0093 S12: -0.1146 S13: -0.2033
REMARK 3 S21: -0.0287 S22: 0.0475 S23: 0.2784
REMARK 3 S31: 0.0383 S32: -0.2596 S33: -0.0382
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: IDEAL-DIST CONTACT TERM CONTACT SETUP.
REMARK 3 RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NI. NUMBER OF
REMARK 3 ATOMS WITH PROPER CCP4 ATOM TYPE=9812. NUMBER WITH APPROX
REMARK 3 DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED
REMARK 3 CONTACTS=5. GERNERALLY MAIN CHAIN ATOMS ARE MODELED BASED ON
REMARK 3 CLEAR ELECTRON DENSITY.HOWEVER,SOME RESIDUES IN THE LOOP REGION,
REMARK 3 WHICH SHOW SMALL GAP IN ELECTRON DENSITY, ARE MODELED
REMARK 3 STEREOCHEMICALLY. SIDE CHAIN ATOMS ARE MODELED BASED ON EITHER
REMARK 3 CLEAR ELECTRON DENSITY, OR STEREOCHEMICALLY WHEN THE ELECTRON
REMARK 3 DENSITY IS NOT DEFINED BUT THE MAIN CHAIN ATOMS OF THAT RESIDUE
REMARK 3 ARE MODELED. THE RESTRAINTS FOR SG85 AND ITS LINK TO PROTEIN
REMARK 3 WERE GENERATED BY GRADE WEBSEVER (GLOBAL PHASING LTD.)
REMARK 4
REMARK 4 2YNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-OCT-12.
REMARK 100 THE DEPOSITION ID IS D_1290054386.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-SEP-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.9
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : BESSY
REMARK 200 BEAMLINE : 14.2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841
REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC, XDS
REMARK 200 DATA SCALING SOFTWARE : AUTOPROC, XDS, SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47447
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960
REMARK 200 RESOLUTION RANGE LOW (A) : 178.670
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 11.10
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 11.30
REMARK 200 R MERGE FOR SHELL (I) : 0.59000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION AT 20C, 6% W/V
REMARK 280 POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2-PROPANOL,
REMARK 280 0.1 M IMIDAZOLE PH 6.9; THEN THE CRYSTAL WAS SOAKED IN THE
REMARK 280 MOTHER LIQUOR SUPPLEMENTED WITH 2MM SG85 FOR 48H, TO GET THE
REMARK 280 COMPLEX CRYSTAL., TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.55667
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 119.11333
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 119.11333
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 59.55667
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 25820 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.2 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 VAL B 303
REMARK 465 VAL B 304
REMARK 465 MET B 305
REMARK 465 GLN B 306
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 ASP A 33 -129.25 48.35
REMARK 500 ASP A 33 -134.42 57.51
REMARK 500 ASP A 51 76.84 -155.87
REMARK 500 ASP B 33 -132.09 53.71
REMARK 500 ASP B 51 76.98 -156.12
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH B2048 DISTANCE = 5.99 ANGSTROMS
REMARK 525 HOH B2078 DISTANCE = 5.81 ANGSTROMS
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 NI A1307 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 41 NE2
REMARK 620 2 CYS A 148 SG 95.4
REMARK 620 3 GLN A 306 OXT 107.9 107.8
REMARK 620 4 HOH A2278 O 126.3 127.1 90.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI A1308 NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 145 SG
REMARK 620 2 HIS A 256 NE2 112.1
REMARK 620 N 1
REMARK 630
REMARK 630 MOLECULE TYPE: NULL
REMARK 630 MOLECULE NAME: N-[(BENZYLOXY)CARBONYL]-O-TERT-BUTYL-L-SERYL-N-{(2R)
REMARK 630 -5-ETHOXY-5-OXO-1-[(3S)-2-OXOPYRROLIDIN-3-YL]PENTAN-2-YL}-L-
REMARK 630 PHENYLALANINAMIDE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 G85 B 501
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: PHQ RZ4 PHE CEV
REMARK 630 DETAILS: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE G85 B 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1307
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1308
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2YNA RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE MAIN PROTEASE OF CORONAVIRUS HKU4
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO BE
REMARK 999 AUTO-CLEAVED BY THE PROTEASE IN THE CRYSTAL, JUDGED BY THE
REMARK 999 ELECTRON DENSITY AT 1.5 A RESOLUTION (FROM THE FREE ENZYME).
DBREF 2YNB A 1 306 UNP P0C6T4 R1A_BCHK4 3292 3597
DBREF 2YNB B 1 306 UNP P0C6T4 R1A_BCHK4 3292 3597
SEQRES 1 A 306 SER GLY LEU VAL LYS MET SER ALA PRO SER GLY ALA VAL
SEQRES 2 A 306 GLU ASN CYS ILE VAL GLN VAL THR CYS GLY SER MET THR
SEQRES 3 A 306 LEU ASN GLY LEU TRP LEU ASP ASN THR VAL TRP CYS PRO
SEQRES 4 A 306 ARG HIS ILE MET CYS PRO ALA ASP GLN LEU THR ASP PRO
SEQRES 5 A 306 ASN TYR ASP ALA LEU LEU ILE SER LYS THR ASN HIS SER
SEQRES 6 A 306 PHE ILE VAL GLN LYS HIS ILE GLY ALA GLN ALA ASN LEU
SEQRES 7 A 306 ARG VAL VAL ALA HIS SER MET VAL GLY VAL LEU LEU LYS
SEQRES 8 A 306 LEU THR VAL ASP VAL ALA ASN PRO SER THR PRO ALA TYR
SEQRES 9 A 306 THR PHE SER THR VAL LYS PRO GLY ALA SER PHE SER VAL
SEQRES 10 A 306 LEU ALA CYS TYR ASN GLY LYS PRO THR GLY VAL PHE THR
SEQRES 11 A 306 VAL ASN LEU ARG HIS ASN SER THR ILE LYS GLY SER PHE
SEQRES 12 A 306 LEU CYS GLY SER CYS GLY SER VAL GLY TYR THR GLU ASN
SEQRES 13 A 306 GLY GLY VAL ILE ASN PHE VAL TYR MET HIS GLN MET GLU
SEQRES 14 A 306 LEU SER ASN GLY THR HIS THR GLY SER SER PHE ASP GLY
SEQRES 15 A 306 VAL MET TYR GLY ALA PHE GLU ASP LYS GLN THR HIS GLN
SEQRES 16 A 306 LEU GLN LEU THR ASP LYS TYR CYS THR ILE ASN VAL VAL
SEQRES 17 A 306 ALA TRP LEU TYR ALA ALA VAL LEU ASN GLY CYS LYS TRP
SEQRES 18 A 306 PHE VAL LYS PRO THR ARG VAL GLY ILE VAL THR TYR ASN
SEQRES 19 A 306 GLU TRP ALA LEU SER ASN GLN PHE THR GLU PHE VAL GLY
SEQRES 20 A 306 THR GLN SER ILE ASP MET LEU ALA HIS ARG THR GLY VAL
SEQRES 21 A 306 SER VAL GLU GLN MET LEU ALA ALA ILE GLN SER LEU HIS
SEQRES 22 A 306 ALA GLY PHE GLN GLY LYS THR ILE LEU GLY GLN SER THR
SEQRES 23 A 306 LEU GLU ASP GLU PHE THR PRO ASP ASP VAL ASN MET GLN
SEQRES 24 A 306 VAL MET GLY VAL VAL MET GLN
SEQRES 1 B 306 SER GLY LEU VAL LYS MET SER ALA PRO SER GLY ALA VAL
SEQRES 2 B 306 GLU ASN CYS ILE VAL GLN VAL THR CYS GLY SER MET THR
SEQRES 3 B 306 LEU ASN GLY LEU TRP LEU ASP ASN THR VAL TRP CYS PRO
SEQRES 4 B 306 ARG HIS ILE MET CYS PRO ALA ASP GLN LEU THR ASP PRO
SEQRES 5 B 306 ASN TYR ASP ALA LEU LEU ILE SER LYS THR ASN HIS SER
SEQRES 6 B 306 PHE ILE VAL GLN LYS HIS ILE GLY ALA GLN ALA ASN LEU
SEQRES 7 B 306 ARG VAL VAL ALA HIS SER MET VAL GLY VAL LEU LEU LYS
SEQRES 8 B 306 LEU THR VAL ASP VAL ALA ASN PRO SER THR PRO ALA TYR
SEQRES 9 B 306 THR PHE SER THR VAL LYS PRO GLY ALA SER PHE SER VAL
SEQRES 10 B 306 LEU ALA CYS TYR ASN GLY LYS PRO THR GLY VAL PHE THR
SEQRES 11 B 306 VAL ASN LEU ARG HIS ASN SER THR ILE LYS GLY SER PHE
SEQRES 12 B 306 LEU CYS GLY SER CYS GLY SER VAL GLY TYR THR GLU ASN
SEQRES 13 B 306 GLY GLY VAL ILE ASN PHE VAL TYR MET HIS GLN MET GLU
SEQRES 14 B 306 LEU SER ASN GLY THR HIS THR GLY SER SER PHE ASP GLY
SEQRES 15 B 306 VAL MET TYR GLY ALA PHE GLU ASP LYS GLN THR HIS GLN
SEQRES 16 B 306 LEU GLN LEU THR ASP LYS TYR CYS THR ILE ASN VAL VAL
SEQRES 17 B 306 ALA TRP LEU TYR ALA ALA VAL LEU ASN GLY CYS LYS TRP
SEQRES 18 B 306 PHE VAL LYS PRO THR ARG VAL GLY ILE VAL THR TYR ASN
SEQRES 19 B 306 GLU TRP ALA LEU SER ASN GLN PHE THR GLU PHE VAL GLY
SEQRES 20 B 306 THR GLN SER ILE ASP MET LEU ALA HIS ARG THR GLY VAL
SEQRES 21 B 306 SER VAL GLU GLN MET LEU ALA ALA ILE GLN SER LEU HIS
SEQRES 22 B 306 ALA GLY PHE GLN GLY LYS THR ILE LEU GLY GLN SER THR
SEQRES 23 B 306 LEU GLU ASP GLU PHE THR PRO ASP ASP VAL ASN MET GLN
SEQRES 24 B 306 VAL MET GLY VAL VAL MET GLN
HET NI A1307 1
HET NI A1308 1
HET G85 B 501 47
HETNAM NI NICKEL (II) ION
HETNAM G85 N-[(BENZYLOXY)CARBONYL]-O-TERT-BUTYL-L-SERYL-N-{(2R)-5-
HETNAM 2 G85 ETHOXY-5-OXO-1-[(3S)-2-OXOPYRROLIDIN-3-YL]PENTAN-2-
HETNAM 3 G85 YL}-L-PHENYLALANINAMIDE
FORMUL 3 NI 2(NI 2+)
FORMUL 5 G85 C35 H48 N4 O8
FORMUL 6 HOH *481(H2 O)
HELIX 1 1 SER A 10 ASN A 15 1 6
HELIX 2 2 HIS A 41 CYS A 44 5 4
HELIX 3 3 ASN A 53 SER A 60 1 8
HELIX 4 4 THR A 62 HIS A 64 5 3
HELIX 5 5 TYR A 185 PHE A 188 5 4
HELIX 6 6 CYS A 203 ASN A 217 1 15
HELIX 7 7 GLY A 229 ASN A 240 1 12
HELIX 8 8 THR A 248 GLY A 259 1 12
HELIX 9 9 SER A 261 GLY A 275 1 15
HELIX 10 10 THR A 292 MET A 301 1 10
HELIX 11 11 SER B 10 ASN B 15 1 6
HELIX 12 12 HIS B 41 CYS B 44 5 4
HELIX 13 13 ASN B 53 SER B 60 1 8
HELIX 14 14 THR B 62 HIS B 64 5 3
HELIX 15 15 TYR B 185 PHE B 188 5 4
HELIX 16 16 CYS B 203 ASN B 217 1 15
HELIX 17 17 GLY B 229 ASN B 240 1 12
HELIX 18 18 THR B 248 GLY B 259 1 12
HELIX 19 19 SER B 261 GLY B 275 1 15
HELIX 20 20 THR B 292 MET B 301 1 10
SHEET 1 AA 7 ALA A 76 LEU A 78 0
SHEET 2 AA 7 PHE A 66 LYS A 70 -1 O VAL A 68 N LEU A 78
SHEET 3 AA 7 ILE A 17 CYS A 22 -1 O GLN A 19 N GLN A 69
SHEET 4 AA 7 MET A 25 LEU A 32 -1 O MET A 25 N CYS A 22
SHEET 5 AA 7 THR A 35 PRO A 39 -1 O THR A 35 N LEU A 32
SHEET 6 AA 7 LEU A 89 VAL A 94 -1 O LEU A 90 N CYS A 38
SHEET 7 AA 7 VAL A 80 VAL A 86 -1 N VAL A 81 O THR A 93
SHEET 1 AB 2 TYR A 104 PHE A 106 0
SHEET 2 AB 2 VAL A 159 SER A 171 1 O ILE A 160 N THR A 105
SHEET 1 AC 5 LYS A 124 ASN A 132 0
SHEET 2 AC 5 SER A 114 TYR A 121 -1 O PHE A 115 N VAL A 131
SHEET 3 AC 5 VAL A 151 ASN A 156 -1 O VAL A 151 N LEU A 118
SHEET 4 AC 5 VAL A 159 SER A 171 -1 O VAL A 159 N ASN A 156
SHEET 5 AC 5 THR A 174 SER A 178 1 O THR A 174 N LEU A 170
SHEET 1 AD 5 LYS A 124 ASN A 132 0
SHEET 2 AD 5 SER A 114 TYR A 121 -1 O PHE A 115 N VAL A 131
SHEET 3 AD 5 VAL A 151 ASN A 156 -1 O VAL A 151 N LEU A 118
SHEET 4 AD 5 VAL A 159 SER A 171 -1 O VAL A 159 N ASN A 156
SHEET 5 AD 5 TYR A 104 PHE A 106 1 O THR A 105 N PHE A 162
SHEET 1 AE 2 THR A 174 SER A 178 0
SHEET 2 AE 2 VAL A 159 SER A 171 1 O MET A 165 N SER A 178
SHEET 1 BA 7 ALA B 76 LEU B 78 0
SHEET 2 BA 7 PHE B 66 LYS B 70 -1 O VAL B 68 N LEU B 78
SHEET 3 BA 7 ILE B 17 CYS B 22 -1 O GLN B 19 N GLN B 69
SHEET 4 BA 7 MET B 25 LEU B 32 -1 O MET B 25 N CYS B 22
SHEET 5 BA 7 THR B 35 PRO B 39 -1 O THR B 35 N LEU B 32
SHEET 6 BA 7 LEU B 89 VAL B 94 -1 O LEU B 90 N CYS B 38
SHEET 7 BA 7 VAL B 80 VAL B 86 -1 N VAL B 81 O THR B 93
SHEET 1 BB 2 TYR B 104 PHE B 106 0
SHEET 2 BB 2 VAL B 159 SER B 171 1 O ILE B 160 N THR B 105
SHEET 1 BC 5 LYS B 124 ASN B 132 0
SHEET 2 BC 5 SER B 114 TYR B 121 -1 O PHE B 115 N VAL B 131
SHEET 3 BC 5 VAL B 151 ASN B 156 -1 O VAL B 151 N LEU B 118
SHEET 4 BC 5 VAL B 159 SER B 171 -1 O VAL B 159 N ASN B 156
SHEET 5 BC 5 THR B 174 SER B 178 1 O THR B 174 N LEU B 170
SHEET 1 BD 5 LYS B 124 ASN B 132 0
SHEET 2 BD 5 SER B 114 TYR B 121 -1 O PHE B 115 N VAL B 131
SHEET 3 BD 5 VAL B 151 ASN B 156 -1 O VAL B 151 N LEU B 118
SHEET 4 BD 5 VAL B 159 SER B 171 -1 O VAL B 159 N ASN B 156
SHEET 5 BD 5 TYR B 104 PHE B 106 1 O THR B 105 N PHE B 162
SHEET 1 BE 2 THR B 174 SER B 178 0
SHEET 2 BE 2 VAL B 159 SER B 171 1 O MET B 165 N SER B 178
LINK SG CYS B 148 C63 G85 B 501 1555 1555 1.82
LINK NE2 HIS A 41 NI NI A1307 1555 1555 2.22
LINK SG CYS A 145 NI NI A1308 1555 1555 2.34
LINK SG CYS A 148 NI NI A1307 1555 1555 2.17
LINK NE2 HIS A 256 NI NI A1308 6655 1555 2.19
LINK OXT GLN A 306 NI NI A1307 6655 1555 1.86
LINK NI NI A1307 O HOH A2278 1555 1555 2.09
SITE 1 AC1 20 MET B 25 THR B 26 HIS B 41 LEU B 49
SITE 2 AC1 20 TYR B 54 PHE B 143 GLY B 146 SER B 147
SITE 3 AC1 20 CYS B 148 HIS B 166 GLN B 167 MET B 168
SITE 4 AC1 20 GLU B 169 LEU B 170 HIS B 175 ASP B 190
SITE 5 AC1 20 LYS B 191 GLN B 192 THR B 193 GLN B 195
SITE 1 AC2 4 HIS A 41 CYS A 148 GLN A 306 HOH A2278
SITE 1 AC3 2 CYS A 145 HIS A 256
CRYST1 79.350 79.350 178.670 90.00 90.00 120.00 P 31 2 1 12
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 0.012602 0.007276 0.000000 0.00000
SCALE2 0.000000 0.014552 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005597 0.00000
MTRIX1 1 -0.975700 0.145900 -0.163300 10.05000 1
MTRIX2 1 0.165100 0.000250 -0.986300 66.06000 1
MTRIX3 1 -0.143800 -0.989300 -0.024330 68.20000 1