HEADER VIRAL PROTEIN/INHIBITOR 01-NOV-21 7VU6 TITLE THE CRYSTAL STRUCTURE OF SARS-COV-2 3CL PROTEASE IN COMPLEX WITH TITLE 2 COMPOUND 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3C-LIKE PROTEINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3CL-PRO,3CLP,MAIN PROTEASE,MPRO,NON-STRUCTURAL PROTEIN 5, COMPND 5 NSP5,SARS CORONAVIRUS MAIN PROTEINASE; COMPND 6 EC: 3.4.22.69; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN-INHIBITO COMPLEX, VIRAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.YAMAMOTO,J.YAMANE,Y.TACHIBANA REVDAT 4 29-NOV-23 7VU6 1 REMARK REVDAT 3 25-MAY-22 7VU6 1 JRNL REVDAT 2 13-APR-22 7VU6 1 JRNL REVDAT 1 06-APR-22 7VU6 0 JRNL AUTH Y.UNOH,S.UEHARA,K.NAKAHARA,H.NOBORI,Y.YAMATSU,S.YAMAMOTO, JRNL AUTH 2 Y.MARUYAMA,Y.TAODA,K.KASAMATSU,T.SUTO,K.KOUKI,A.NAKAHASHI, JRNL AUTH 3 S.KAWASHIMA,T.SANAKI,S.TOBA,K.UEMURA,T.MIZUTARE,S.ANDO, JRNL AUTH 4 M.SASAKI,Y.ORBA,H.SAWA,A.SATO,T.SATO,T.KATO,Y.TACHIBANA JRNL TITL DISCOVERY OF S-217622, A NONCOVALENT ORAL SARS-COV-2 3CL JRNL TITL 2 PROTEASE INHIBITOR CLINICAL CANDIDATE FOR TREATING COVID-19. JRNL REF J.MED.CHEM. V. 65 6499 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35352927 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00117 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 52687 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2669 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3961 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4509 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : 0.30000 REMARK 3 B33 (A**2) : 0.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.86000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.157 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.768 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.887 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4705 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6425 ; 1.796 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.432 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;38.329 ;24.898 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 711 ;13.995 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;11.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 725 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3611 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7VU6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025401. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-X REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56021 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 55.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42900 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: 6Y2E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 49.61450 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 GLY A 2 REMARK 465 SER A 301 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 GLY B -1 REMARK 465 SER B 0 REMARK 465 SER B 1 REMARK 465 GLY B 2 REMARK 465 GLY B 302 REMARK 465 VAL B 303 REMARK 465 THR B 304 REMARK 465 PHE B 305 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 GLU A 47 CG CD OE1 OE2 REMARK 470 LEU A 50 CG CD1 CD2 REMARK 470 LEU A 67 CG CD1 CD2 REMARK 470 GLN A 69 CG CD OE1 NE2 REMARK 470 ASN A 72 CG OD1 ND2 REMARK 470 VAL A 73 CG1 CG2 REMARK 470 GLN A 74 CD OE1 NE2 REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 90 CE NZ REMARK 470 LYS A 97 CE NZ REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 137 NZ REMARK 470 TYR A 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 155 CG OD1 OD2 REMARK 470 ARG A 188 CZ NH1 NH2 REMARK 470 ARG A 222 NE CZ NH1 NH2 REMARK 470 PHE A 223 CD1 CD2 CE1 CE2 CZ REMARK 470 ASN A 238 OD1 ND2 REMARK 470 ASN A 277 CG OD1 ND2 REMARK 470 LEU A 286 CD1 CD2 REMARK 470 GLU A 288 CD OE1 OE2 REMARK 470 ARG A 298 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 59 CG1 CG2 CD1 REMARK 470 ARG B 60 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 90 CE NZ REMARK 470 LYS B 100 CD CE NZ REMARK 470 LYS B 137 CD CE NZ REMARK 470 ASP B 153 CG OD1 OD2 REMARK 470 TYR B 154 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 188 CZ NH1 NH2 REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 223 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 236 CD CE NZ REMARK 470 ASN B 277 CG OD1 ND2 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 745 O HOH A 751 1.73 REMARK 500 O HOH A 740 O HOH B 765 1.97 REMARK 500 O HOH B 768 O HOH B 778 2.09 REMARK 500 O HOH A 725 O HOH B 765 2.15 REMARK 500 CD2 PHE B 294 O HOH B 733 2.16 REMARK 500 O CYS A 300 O HOH A 601 2.18 REMARK 500 O HOH B 610 O HOH B 725 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 187 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES 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 -125.87 47.86 REMARK 500 ASN A 51 74.53 -157.30 REMARK 500 ASN A 84 -127.06 52.32 REMARK 500 TYR A 154 70.42 41.52 REMARK 500 ASP A 155 -6.12 64.70 REMARK 500 PRO A 184 35.14 -85.19 REMARK 500 ASP B 33 -132.92 53.17 REMARK 500 ASN B 51 76.97 -153.91 REMARK 500 ASN B 84 -123.50 47.99 REMARK 500 TYR B 154 -105.04 69.00 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 793 DISTANCE = 6.04 ANGSTROMS DBREF 7VU6 A 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 DBREF 7VU6 B 1 306 UNP P0DTC1 R1A_SARS2 3264 3569 SEQADV 7VU6 GLY A -1 UNP P0DTC1 EXPRESSION TAG SEQADV 7VU6 SER A 0 UNP P0DTC1 EXPRESSION TAG SEQADV 7VU6 GLY B -1 UNP P0DTC1 EXPRESSION TAG SEQADV 7VU6 SER B 0 UNP P0DTC1 EXPRESSION TAG SEQRES 1 A 308 GLY SER 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 GLY SER 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 HET 7YY A 501 37 HET 7YY B 501 37 HETNAM 7YY 6-[(6-CHLORANYL-2-METHYL-INDAZOL-5-YL)AMINO]-3-[(1- HETNAM 2 7YY METHYL-1,2,4-TRIAZOL-3-YL)METHYL]-1-[[2,4,5- HETNAM 3 7YY TRIS(FLUORANYL)PHENYL]METHYL]-1,3,5-TRIAZINE-2,4-DIONE FORMUL 3 7YY 2(C22 H17 CL F3 N9 O2) FORMUL 5 HOH *350(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 THR A 45 LEU A 50 1 6 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 CYS A 300 1 9 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 HIS B 64 5 3 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 GLN A 83 O VAL A 86 SHEET 1 AA2 5 LYS A 100 PHE A 103 0 SHEET 2 AA2 5 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 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 TYR A 126 N VAL A 114 SHEET 1 AA3 3 LYS A 100 PHE A 103 0 SHEET 2 AA3 3 CYS A 156 GLU A 166 1 O VAL A 157 N LYS A 100 SHEET 3 AA3 3 HIS A 172 THR A 175 -1 O ALA A 173 N MET A 165 SHEET 1 AA4 7 VAL B 73 LEU B 75 0 SHEET 2 AA4 7 PHE B 66 ALA B 70 -1 N ALA B 70 O VAL B 73 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 THR B 25 N CYS B 22 SHEET 5 AA4 7 VAL B 35 PRO B 39 -1 O TYR B 37 N LEU B 30 SHEET 6 AA4 7 VAL B 86 VAL B 91 -1 O LEU B 89 N VAL B 36 SHEET 7 AA4 7 VAL B 77 GLN B 83 -1 N ILE B 78 O LYS B 90 SHEET 1 AA5 5 LYS B 100 PHE B 103 0 SHEET 2 AA5 5 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 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 SER B 123 N ALA B 116 SHEET 1 AA6 3 LYS B 100 PHE B 103 0 SHEET 2 AA6 3 CYS B 156 GLU B 166 1 O VAL B 157 N LYS B 100 SHEET 3 AA6 3 HIS B 172 THR B 175 -1 O ALA B 173 N MET B 165 CRYST1 55.468 99.229 58.883 90.00 108.05 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 0.018028 0.000000 0.005874 0.00000 SCALE2 0.000000 0.010078 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017862 0.00000