HEADER HYDROLASE/HYDROLASE INHIBITOR 05-JUN-20 6XBG TITLE CRYSTAL STRUCTURE OF THE SARS-COV-2 (COVID-19) MAIN PROTEASE IN TITLE 2 COMPLEX WITH INHIBITOR UAW246 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 3264-3569; COMPND 5 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 6 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 7 EC: 3.4.22.69; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: INHIBITOR UAW246; COMPND 11 CHAIN: C, E; COMPND 12 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; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS COVID, COVID19, COVID-19, SARS, SARS COV2, COV, NCOV 19, CORONAVIRUS, KEYWDS 2 MAIN PROTEASE, 3CL, MPRO, PRO, VIRAL PROTEIN, GC376, CALPAIN KEYWDS 3 INHIBITOR II, LEUPEPTIN, CALPAIN, ALDEHYDE, GC-376, 3CL-LIKE, A- KEYWDS 4 KETOAMIDE, UAW41, UAW246, UAW247, UAW248, 246, 247, 248, KEYWDS 5 ALPHEKETOAMIDE, ALPHA, KETOAMIDE, PEPTIDOMIMETIC, PROTEASE, KEYWDS 6 CYSTEINE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.SACCO,C.MA,J.WANG,Y.CHEN REVDAT 6 15-NOV-23 6XBG 1 LINK ATOM REVDAT 5 18-OCT-23 6XBG 1 REMARK REVDAT 4 27-JAN-21 6XBG 1 COMPND REVDAT 3 23-DEC-20 6XBG 1 JRNL REVDAT 2 18-NOV-20 6XBG 1 JRNL REVDAT 1 17-JUN-20 6XBG 0 JRNL AUTH M.D.SACCO,C.MA,P.LAGARIAS,A.GAO,J.A.TOWNSEND,X.MENG,P.DUBE, JRNL AUTH 2 X.ZHANG,Y.HU,N.KITAMURA,B.HURST,B.TARBET,M.T.MARTY, JRNL AUTH 3 A.KOLOCOURIS,Y.XIANG,Y.CHEN,J.WANG JRNL TITL STRUCTURE AND INHIBITION OF THE SARS-COV-2 MAIN PROTEASE JRNL TITL 2 REVEAL STRATEGY FOR DEVELOPING DUAL INHIBITORS AGAINST M PRO JRNL TITL 3 AND CATHEPSIN L. JRNL REF SCI ADV V. 6 2020 JRNL REFN ESSN 2375-2548 JRNL PMID 33158912 JRNL DOI 10.1126/SCIADV.ABE0751 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 99703 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5297 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7130 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 382 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4728 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.81000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.431 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5067 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4544 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6907 ; 1.832 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10579 ; 1.499 ; 1.586 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 7.512 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 244 ;33.748 ;23.197 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 801 ;13.443 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;14.986 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 657 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5798 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1067 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6XBG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249884. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 105029 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 1.06300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 7BRR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3000, 0.1 M SODIUM CITRATE, PH REMARK 280 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 49.42700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, E 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE UAW246 IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: UAW246 REMARK 400 CHAIN: C, E 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 HIS A -1 REMARK 465 MET A 0 REMARK 465 SER A 1 REMARK 465 GLY A 302 REMARK 465 VAL A 303 REMARK 465 THR A 304 REMARK 465 PHE A 305 REMARK 465 GLN A 306 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 GLN B 306 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 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 -124.39 52.53 REMARK 500 ASN A 51 67.30 -157.38 REMARK 500 ASN A 84 -126.58 57.07 REMARK 500 TYR A 154 -112.14 66.04 REMARK 500 TYR A 154 -112.14 57.63 REMARK 500 PRO A 184 30.14 -83.82 REMARK 500 THR B 24 -28.21 83.13 REMARK 500 ASP B 33 -132.08 52.45 REMARK 500 ASN B 84 -122.61 55.59 REMARK 500 ASP B 155 -0.46 61.29 REMARK 500 THR B 190 -168.76 -116.85 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 B 815 DISTANCE = 7.73 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 504 DBREF 6XBG A 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 6XBG B 1 306 UNP P0DTD1 R1AB_SARS2 3264 3569 DBREF 6XBG C 1 4 PDB 6XBG 6XBG 1 4 DBREF 6XBG E 1 4 PDB 6XBG 6XBG 1 4 SEQADV 6XBG HIS A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 6XBG MET A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 6XBG HIS B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 6XBG MET B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 308 HIS MET SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY SEQRES 2 A 308 LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR SEQRES 3 A 308 THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR SEQRES 4 A 308 CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU SEQRES 5 A 308 ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN SEQRES 6 A 308 HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG SEQRES 7 A 308 VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU SEQRES 8 A 308 LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS SEQRES 9 A 308 PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU SEQRES 10 A 308 ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS SEQRES 11 A 308 ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU SEQRES 12 A 308 ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR SEQRES 13 A 308 ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU SEQRES 14 A 308 PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN SEQRES 15 A 308 PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA SEQRES 16 A 308 ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU ALA SEQRES 17 A 308 TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE SEQRES 18 A 308 LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU SEQRES 19 A 308 VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP SEQRES 20 A 308 HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY SEQRES 21 A 308 ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU SEQRES 22 A 308 LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER SEQRES 23 A 308 ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL SEQRES 24 A 308 ARG GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 B 308 HIS MET SER GLY PHE ARG LYS MET ALA PHE PRO SER GLY SEQRES 2 B 308 LYS VAL GLU GLY CYS MET VAL GLN VAL THR CYS GLY THR SEQRES 3 B 308 THR THR LEU ASN GLY LEU TRP LEU ASP ASP VAL VAL TYR SEQRES 4 B 308 CYS PRO ARG HIS VAL ILE CYS THR SER GLU ASP MET LEU SEQRES 5 B 308 ASN PRO ASN TYR GLU ASP LEU LEU ILE ARG LYS SER ASN SEQRES 6 B 308 HIS ASN PHE LEU VAL GLN ALA GLY ASN VAL GLN LEU ARG SEQRES 7 B 308 VAL ILE GLY HIS SER MET GLN ASN CYS VAL LEU LYS LEU SEQRES 8 B 308 LYS VAL ASP THR ALA ASN PRO LYS THR PRO LYS TYR LYS SEQRES 9 B 308 PHE VAL ARG ILE GLN PRO GLY GLN THR PHE SER VAL LEU SEQRES 10 B 308 ALA CYS TYR ASN GLY SER PRO SER GLY VAL TYR GLN CYS SEQRES 11 B 308 ALA MET ARG PRO ASN PHE THR ILE LYS GLY SER PHE LEU SEQRES 12 B 308 ASN GLY SER CYS GLY SER VAL GLY PHE ASN ILE ASP TYR SEQRES 13 B 308 ASP CYS VAL SER PHE CYS TYR MET HIS HIS MET GLU LEU SEQRES 14 B 308 PRO THR GLY VAL HIS ALA GLY THR ASP LEU GLU GLY ASN SEQRES 15 B 308 PHE TYR GLY PRO PHE VAL ASP ARG GLN THR ALA GLN ALA SEQRES 16 B 308 ALA GLY THR ASP THR THR ILE THR VAL ASN VAL LEU ALA SEQRES 17 B 308 TRP LEU TYR ALA ALA VAL ILE ASN GLY ASP ARG TRP PHE SEQRES 18 B 308 LEU ASN ARG PHE THR THR THR LEU ASN ASP PHE ASN LEU SEQRES 19 B 308 VAL ALA MET LYS TYR ASN TYR GLU PRO LEU THR GLN ASP SEQRES 20 B 308 HIS VAL ASP ILE LEU GLY PRO LEU SER ALA GLN THR GLY SEQRES 21 B 308 ILE ALA VAL LEU ASP MET CYS ALA SER LEU LYS GLU LEU SEQRES 22 B 308 LEU GLN ASN GLY MET ASN GLY ARG THR ILE LEU GLY SER SEQRES 23 B 308 ALA LEU LEU GLU ASP GLU PHE THR PRO PHE ASP VAL VAL SEQRES 24 B 308 ARG GLN CYS SER GLY VAL THR PHE GLN SEQRES 1 C 4 P6S LEU UZ4 UZ1 SEQRES 1 E 4 P6S LEU UZ4 UZ1 HET P6S C 1 10 HET UZ4 C 3 13 HET UZ1 C 4 4 HET P6S E 1 10 HET UZ4 E 3 13 HET UZ1 E 4 4 HET GOL B 501 12 HET GOL B 502 6 HET GOL B 503 6 HET NA B 504 1 HETNAM P6S BENZYL HYDROGEN CARBONATE HETNAM UZ4 (2R,3S)-3-AMINO-2-HYDROXY-4-[(3S)-2-OXOPYRROLIDIN-3- HETNAM 2 UZ4 YL]BUTANOIC ACID HETNAM UZ1 CYCLOPROPANAMINE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 P6S 2(C8 H8 O3) FORMUL 3 UZ4 2(C8 H14 N2 O4) FORMUL 3 UZ1 2(C3 H7 N) FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 NA NA 1+ FORMUL 9 HOH *400(H2 O) HELIX 1 AA1 SER A 10 GLY A 15 1 6 HELIX 2 AA2 HIS A 41 CYS A 44 5 4 HELIX 3 AA3 GLU A 47 ASN A 51 5 5 HELIX 4 AA4 ASN A 53 ARG A 60 1 8 HELIX 5 AA5 SER A 62 PHE A 66 5 5 HELIX 6 AA6 ILE A 200 ASN A 214 1 15 HELIX 7 AA7 THR A 226 TYR A 237 1 12 HELIX 8 AA8 THR A 243 LEU A 250 1 8 HELIX 9 AA9 LEU A 250 GLY A 258 1 9 HELIX 10 AB1 ALA A 260 GLY A 275 1 16 HELIX 11 AB2 THR A 292 SER A 301 1 10 HELIX 12 AB3 SER B 10 GLY B 15 1 6 HELIX 13 AB4 HIS B 41 CYS B 44 5 4 HELIX 14 AB5 THR B 45 MET B 49 5 5 HELIX 15 AB6 ASN B 53 ARG B 60 1 8 HELIX 16 AB7 SER B 62 PHE B 66 5 5 HELIX 17 AB8 ILE B 200 ASN B 214 1 15 HELIX 18 AB9 THR B 226 TYR B 237 1 12 HELIX 19 AC1 THR B 243 LEU B 250 1 8 HELIX 20 AC2 LEU B 250 GLY B 258 1 9 HELIX 21 AC3 ALA B 260 GLY B 275 1 16 HELIX 22 AC4 THR B 292 SER B 301 1 10 SHEET 1 AA1 7 VAL A 73 LEU A 75 0 SHEET 2 AA1 7 LEU A 67 ALA A 70 -1 N ALA A 70 O VAL A 73 SHEET 3 AA1 7 MET A 17 CYS A 22 -1 N THR A 21 O LEU A 67 SHEET 4 AA1 7 THR A 25 LEU A 32 -1 O LEU A 27 N VAL A 20 SHEET 5 AA1 7 VAL A 35 PRO A 39 -1 O TYR A 37 N LEU A 30 SHEET 6 AA1 7 VAL A 86 VAL A 91 -1 O LEU A 87 N CYS A 38 SHEET 7 AA1 7 VAL A 77 GLN A 83 -1 N SER A 81 O LYS A 88 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA2 5 VAL A 148 ASP A 153 -1 N ASN A 151 O SER A 158 SHEET 4 AA2 5 THR A 111 TYR A 118 -1 N SER A 113 O PHE A 150 SHEET 5 AA2 5 SER A 121 ALA A 129 -1 O SER A 123 N ALA A 116 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O PHE A 159 N LYS A 102 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O THR A 175 N MET A 162 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 LEU B 67 ALA B 70 -1 N VAL B 68 O LEU B 75 SHEET 3 AA4 7 MET B 17 CYS B 22 -1 N THR B 21 O LEU B 67 SHEET 4 AA4 7 THR B 25 LEU B 32 -1 O LEU B 27 N VAL B 20 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O VAL B 35 N LEU B 32 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 87 N CYS B 38 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N SER B 81 O LYS B 88 SHEET 1 AA5 5 LYS B 100 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA5 5 VAL B 148 ASP B 153 -1 N ASN B 151 O SER B 158 SHEET 4 AA5 5 THR B 111 TYR B 118 -1 N SER B 113 O PHE B 150 SHEET 5 AA5 5 SER B 121 ALA B 129 -1 O TYR B 126 N VAL B 114 SHEET 1 AA6 3 LYS B 100 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O PHE B 159 N LYS B 102 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 LINK SG CYS A 145 C28 UZ4 C 3 1555 1555 1.72 LINK SG CYS B 145 C28 UZ4 E 3 1555 1555 1.74 LINK C19 P6S C 1 N LEU C 2 1555 1555 1.27 LINK C LEU C 2 N UZ4 C 3 1555 1555 1.32 LINK C UZ4 C 3 N33 UZ1 C 4 1555 1555 1.41 LINK C19 P6S E 1 N LEU E 2 1555 1555 1.40 LINK C LEU E 2 N UZ4 E 3 1555 1555 1.37 LINK C UZ4 E 3 N33 UZ1 E 4 1555 1555 1.37 SITE 1 AC1 3 SER B 62 ASN B 63 HIS B 64 SITE 1 AC2 6 GLU B 14 GLY B 15 MET B 17 LYS B 97 SITE 2 AC2 6 HOH B 694 HOH B 705 SITE 1 AC3 6 LYS A 5 HOH A 420 PHE B 3 ARG B 4 SITE 2 AC3 6 LYS B 5 HOH B 650 SITE 1 AC4 1 LEU B 271 CRYST1 55.367 98.854 59.215 90.00 108.23 90.00 P 1 21 1 4 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 0.018061 0.000000 0.005949 0.00000 SCALE2 0.000000 0.010116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017780 0.00000