HEADER HYDROLASE 13-OCT-12 2YNA TITLE CRYSTAL STRUCTURE OF THE MAIN PROTEASE OF CORONAVIRUS HKU4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO, 3CLP, NSP5; COMPND 5 EC: 3.4.22.69, 3.4.22.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TYLONYCTERIS BAT CORONAVIRUS HKU4; SOURCE 3 ORGANISM_TAXID: 694007; SOURCE 4 STRAIN: HKU4-1L; 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 EXPDTA X-RAY DIFFRACTION AUTHOR Q.MA,Y.XIAO,R.HILGENFELD REVDAT 3 20-DEC-23 2YNA 1 REMARK LINK REVDAT 2 15-MAY-19 2YNA 1 REMARK REVDAT 1 23-OCT-13 2YNA 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. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 105041 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5247 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.54 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.54 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 7456 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1790 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7069 REMARK 3 BIN R VALUE (WORKING SET) : 0.1783 REMARK 3 BIN FREE R VALUE : 0.1913 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.19 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 387 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 : 31 REMARK 3 SOLVENT ATOMS : 827 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.56090 REMARK 3 B22 (A**2) : -0.56090 REMARK 3 B33 (A**2) : 1.12180 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) : 0.157 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.063 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.062 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.069 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.060 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 : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 9413 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 16930 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2067 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 114 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1455 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 9413 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 2 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 650 ; 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 : 10981 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.11 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.68 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 14.11 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 AND RESID 1-306 REMARK 3 ORIGIN FOR THE GROUP (A): 16.9335 51.2728 27.4749 REMARK 3 T TENSOR REMARK 3 T11: -0.0438 T22: -0.0547 REMARK 3 T33: -0.0659 T12: 0.0236 REMARK 3 T13: 0.0039 T23: 0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.6766 L22: 0.2504 REMARK 3 L33: 0.7573 L12: -0.0373 REMARK 3 L13: -0.4720 L23: -0.0067 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: -0.0224 S13: -0.0222 REMARK 3 S21: 0.0122 S22: -0.0033 S23: -0.0505 REMARK 3 S31: 0.0363 S32: 0.0171 S33: 0.0285 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN BAND RESID 1-302 REMARK 3 ORIGIN FOR THE GROUP (A): -3.5831 41.7142 14.9508 REMARK 3 T TENSOR REMARK 3 T11: 0.0111 T22: 0.0334 REMARK 3 T33: 0.0237 T12: 0.0069 REMARK 3 T13: 0.0164 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 1.3334 L22: 0.7909 REMARK 3 L33: 0.5983 L12: -0.5254 REMARK 3 L13: 0.2156 L23: -0.1795 REMARK 3 S TENSOR REMARK 3 S11: -0.0166 S12: -0.0691 S13: -0.1668 REMARK 3 S21: 0.0265 S22: 0.0434 S23: 0.1905 REMARK 3 S31: 0.0135 S32: -0.1042 S33: -0.0268 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGEN ATOMS AT THEORETICAL THE REMARK 3 REFINEMENT BUT REMOVED IN THIS DEPOSITED PDB. GERNERALLY MAIN REMARK 3 CHAIN ATOMS ARE MODELED BASED ON CLEAR ELECTRON DENSITY.HOWEVER, REMARK 3 SOME RESIDUES IN THE LOOP REGION, WHICH SHOW SMALL GAP IN REMARK 3 ELECTRON DENSITY, ARE MODELED STEREOCHEMICALLY. SIDE CHAIN ATOMS REMARK 3 ARE MODELED BASED ON EITHER CLEAR ELECTRON DENSITY, OR REMARK 3 STEREOCHEMICALLY WHEN THE ELECTRON DENSITY IS NOT DEFINED BUT REMARK 3 THE MAIN CHAIN ATOMS OF THAT RESIDUE ARE MODELED. REMARK 4 REMARK 4 2YNA 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_1290054384. 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 : 105128 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 178.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 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: PDB ENTRY 3TNT 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: SITTING-DROP VAPOR DIFFUSION AT 20C, REMARK 280 6% W/V POLYETHYLENE GLYCOL 3350, 2% V/V TACSIMATE, 5% V/V 2- REMARK 280 PROPANOL, 0.1 M IMIDAZOLE PH 6.9., VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 59.45667 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 118.91333 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 118.91333 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 59.45667 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.8 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: 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 2301 O HOH A 2302 1.81 REMARK 500 O HOH A 2442 O HOH A 2443 2.04 REMARK 500 O HOH A 2095 O HOH A 2247 2.09 REMARK 500 O HOH B 2180 O HOH B 2194 2.17 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 ASP A 33 -133.27 54.56 REMARK 500 ASP B 33 -131.72 57.34 REMARK 500 ASP B 51 72.60 -156.60 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 A2080 DISTANCE = 7.20 ANGSTROMS REMARK 525 HOH A2128 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A2147 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A2164 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A2165 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A2166 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH B2073 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH B2116 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B2208 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B2352 DISTANCE = 7.84 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 105.4 REMARK 620 3 GLN A 306 OXT 99.2 110.3 REMARK 620 4 IMD A1308 N3 104.1 133.6 99.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B1303 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 41 NE2 REMARK 620 2 CYS B 148 SG 111.2 REMARK 620 3 HOH B2075 O 104.5 119.8 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 1308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YNB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE MAIN PROTEASE OF CORONAVIRUS HKU4 IN REMARK 900 COMPLEX WITH A MICHAEL ACCEPTOR SG85 REMARK 999 REMARK 999 SEQUENCE REMARK 999 5XHIS TAG AT THE C-TERMINUS WAS DESIGNED, BUT IT SEEMS TO REMARK 999 BE AUTO-CLEAVED BY THE PROTEASE IN THE CRYSTAL, JUDGED BY REMARK 999 THE ELECTRON DENSITY AT 1.5 A RESOLUTION. SO THIS TAG IS REMARK 999 INCLUDED IN THE INPUT SEQUENCE. DBREF 2YNA A 1 306 UNP P0C6T4 R1A_BCHK4 3292 3597 DBREF 2YNA 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 IMD A1308 5 HET GOL A1309 6 HET NI B1303 1 HET GOL B1304 6 HET GOL B1305 6 HET GOL B1306 6 HETNAM NI NICKEL (II) ION HETNAM IMD IMIDAZOLE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NI 2(NI 2+) FORMUL 4 IMD C3 H5 N2 1+ FORMUL 5 GOL 4(C3 H8 O3) FORMUL 10 HOH *827(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 PRO A 45 LEU A 49 5 5 HELIX 4 4 ASN A 53 SER A 60 1 8 HELIX 5 5 THR A 62 PHE A 66 5 5 HELIX 6 6 TYR A 185 PHE A 188 5 4 HELIX 7 7 CYS A 203 ASN A 217 1 15 HELIX 8 8 GLY A 229 ASN A 240 1 12 HELIX 9 9 THR A 248 GLY A 259 1 12 HELIX 10 10 SER A 261 GLY A 275 1 15 HELIX 11 11 THR A 292 MET A 301 1 10 HELIX 12 12 SER B 10 ASN B 15 1 6 HELIX 13 13 HIS B 41 CYS B 44 5 4 HELIX 14 14 PRO B 45 LEU B 49 5 5 HELIX 15 15 ASN B 53 SER B 60 1 8 HELIX 16 16 THR B 62 HIS B 64 5 3 HELIX 17 17 TYR B 185 PHE B 188 5 4 HELIX 18 18 CYS B 203 ASN B 217 1 15 HELIX 19 19 GLY B 229 ASN B 240 1 12 HELIX 20 20 THR B 248 GLY B 259 1 12 HELIX 21 21 SER B 261 GLY B 275 1 15 HELIX 22 22 THR B 292 GLN B 299 1 8 SHEET 1 AA 6 ILE A 67 GLN A 69 0 SHEET 2 AA 6 ILE A 17 CYS A 22 -1 O GLN A 19 N GLN A 69 SHEET 3 AA 6 MET A 25 LEU A 32 -1 O MET A 25 N CYS A 22 SHEET 4 AA 6 THR A 35 PRO A 39 -1 O THR A 35 N LEU A 32 SHEET 5 AA 6 LEU A 89 VAL A 94 -1 O LEU A 90 N CYS A 38 SHEET 6 AA 6 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 NE2 HIS A 41 NI NI A1307 1555 1555 2.22 LINK SG CYS A 148 NI NI A1307 1555 1555 2.24 LINK OXT GLN A 306 NI NI A1307 6655 1555 1.95 LINK NI NI A1307 N3 IMD A1308 1555 1555 1.99 LINK NE2 HIS B 41 NI NI B1303 1555 1555 1.89 LINK SG CYS B 148 NI NI B1303 1555 1555 2.47 LINK NI NI B1303 O HOH B2075 1555 1555 2.69 SITE 1 AC1 5 LEU A 27 HIS A 41 CYS A 148 GLN A 306 SITE 2 AC1 5 IMD A1308 SITE 1 AC2 3 HIS B 41 CYS B 148 HOH B2075 SITE 1 AC3 4 LEU A 27 HIS A 41 GLN A 306 NI A1307 SITE 1 AC4 9 THR A 126 HOH A2275 ALA B 8 ASP B 295 SITE 2 AC4 9 HOH B2014 HOH B2213 HOH B2214 HOH B2344 SITE 3 AC4 9 HOH B2345 SITE 1 AC5 11 MET A 6 ALA A 8 GLU A 155 MET A 298 SITE 2 AC5 11 HOH A2014 HOH A2307 HOH A2308 HOH A2311 SITE 3 AC5 11 HOH A2466 HOH A2467 THR B 126 SITE 1 AC6 8 SER B 107 THR B 108 SER B 179 ASP B 181 SITE 2 AC6 8 HOH B2169 HOH B2171 HOH B2349 HOH B2351 SITE 1 AC7 5 ASN A 15 HOH A2023 GLY B 11 GLU B 14 SITE 2 AC7 5 ASN B 15 CRYST1 79.624 79.624 178.370 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 0.012559 0.007251 0.000000 0.00000 SCALE2 0.000000 0.014502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005606 0.00000 MTRIX1 1 -0.974000 0.147900 -0.171500 10.17000 1 MTRIX2 1 0.173800 0.002775 -0.984800 66.33000 1 MTRIX3 1 -0.145200 -0.989000 -0.028410 68.57000 1