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 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 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