HEADER VIRAL PROTEIN 31-DEC-20 7BF6 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MACRODOMAIN IN COMPLEX WITH REMDESIVIR TITLE 2 METABOLITE GS-441524 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN-LIKE PROTEASE NSP3; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NON-STRUCTURAL PROTEIN 3,NSP3,PL2-PRO,PAPAIN-LIKE COMPND 5 PROTEINASE,PL-PRO; COMPND 6 EC: 3.4.19.12,3.4.22.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 GENE: REP, 1A-1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: -R3-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS NSP3, MACRODOMAIN, SARS-COV-2, REMDESIVIR, GS-441524, COVID-19, KEYWDS 2 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, VIRAL KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.NI,S.KNAPP,A.CHAIKUAD,STRUCTURAL GENOMICS CONSORTIUM,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 5 31-JAN-24 7BF6 1 REMARK REVDAT 4 27-JUL-22 7BF6 1 COMPND SOURCE HETSYN REVDAT 3 07-JUL-21 7BF6 1 JRNL REVDAT 2 27-JAN-21 7BF6 1 COMPND REMARK HET HETNAM REVDAT 2 2 1 HETSYN FORMUL SITE ATOM REVDAT 1 13-JAN-21 7BF6 0 JRNL AUTH X.NI,M.SCHRODER,V.OLIERIC,M.E.SHARPE,V.HERNANDEZ-OLMOS, JRNL AUTH 2 E.PROSCHAK,D.MERK,S.KNAPP,A.CHAIKUAD JRNL TITL STRUCTURAL INSIGHTS INTO PLASTICITY AND DISCOVERY OF JRNL TITL 2 REMDESIVIR METABOLITE GS-441524 BINDING IN SARS-COV-2 JRNL TITL 3 MACRODOMAIN. JRNL REF ACS MED.CHEM.LETT. V. 12 603 2021 JRNL REFN ISSN 1948-5875 JRNL PMID 33850605 JRNL DOI 10.1021/ACSMEDCHEMLETT.0C00684 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 24153 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) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1286 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1754 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3838 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : -1.59000 REMARK 3 B33 (A**2) : 0.36000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.21000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.285 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.167 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.146 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3988 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3835 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5415 ; 1.372 ; 1.640 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8816 ; 1.308 ; 1.594 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 504 ; 7.618 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;38.819 ;25.385 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 656 ;14.352 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.149 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 516 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4716 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 844 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 4 171 B 4 171 5144 0.110 0.050 REMARK 3 2 A 4 167 C 4 167 5122 0.090 0.050 REMARK 3 3 B 2 167 C 2 167 5172 0.080 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 172 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2808 -10.0318 0.6834 REMARK 3 T TENSOR REMARK 3 T11: 0.0219 T22: 0.1447 REMARK 3 T33: 0.1272 T12: -0.0107 REMARK 3 T13: 0.0498 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 1.3341 L22: 0.7842 REMARK 3 L33: 0.5810 L12: -0.0440 REMARK 3 L13: -0.1086 L23: -0.2028 REMARK 3 S TENSOR REMARK 3 S11: -0.0723 S12: 0.0113 S13: -0.0665 REMARK 3 S21: -0.0093 S22: 0.0024 S23: 0.0279 REMARK 3 S31: 0.0449 S32: -0.0277 S33: 0.0698 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 172 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6669 0.8538 -28.1638 REMARK 3 T TENSOR REMARK 3 T11: 0.2642 T22: 0.1547 REMARK 3 T33: 0.0092 T12: -0.1166 REMARK 3 T13: -0.0373 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 1.4744 L22: 3.6793 REMARK 3 L33: 3.8618 L12: 0.1529 REMARK 3 L13: -0.8199 L23: -0.2560 REMARK 3 S TENSOR REMARK 3 S11: -0.2708 S12: -0.1494 S13: 0.0510 REMARK 3 S21: -0.8166 S22: 0.3923 S23: 0.1434 REMARK 3 S31: 0.0382 S32: -0.0317 S33: -0.1215 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 168 REMARK 3 ORIGIN FOR THE GROUP (A): 43.5386 -13.3127 -34.4436 REMARK 3 T TENSOR REMARK 3 T11: 0.1832 T22: 0.0801 REMARK 3 T33: 0.0544 T12: 0.0187 REMARK 3 T13: -0.0597 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 0.9021 L22: 5.5691 REMARK 3 L33: 5.4639 L12: -1.1553 REMARK 3 L13: 1.1568 L23: -3.2133 REMARK 3 S TENSOR REMARK 3 S11: 0.1515 S12: -0.1060 S13: -0.1582 REMARK 3 S21: -0.6865 S22: 0.1789 S23: 0.5244 REMARK 3 S31: 0.1566 S32: -0.0900 S33: -0.3303 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7BF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1292113250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00003 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25440 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 48.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.75500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6YWK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M SODIUM ACETATE, REMARK 280 0.1 M TRIS, PH 8.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 78.61900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.23800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.61900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.23800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 0 REMARK 465 HIS A 1 REMARK 465 MET A 2 REMARK 465 VAL A 3 REMARK 465 GLY B 0 REMARK 465 HIS B 1 REMARK 465 GLY C 0 REMARK 465 HIS C 1 REMARK 465 LEU C 169 REMARK 465 GLU C 170 REMARK 465 MET C 171 REMARK 465 LYS C 172 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 ASN A 4 CG OD1 ND2 REMARK 470 MET C 2 CG SD CE 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 SER A 5 134.79 83.13 REMARK 500 ASN A 59 -0.37 75.61 REMARK 500 HIS A 86 -125.60 51.32 REMARK 500 ASN B 59 -1.59 78.51 REMARK 500 HIS B 86 -126.77 54.11 REMARK 500 ASN C 59 -1.27 77.99 REMARK 500 HIS C 86 -126.32 51.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U08 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U08 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue U08 C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 203 DBREF 7BF6 A 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 DBREF 7BF6 B 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 DBREF 7BF6 C 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 SEQADV 7BF6 GLY A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 HIS A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 MET A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 GLY B 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 HIS B 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 MET B 2 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 GLY C 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 HIS C 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF6 MET C 2 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 173 GLY HIS MET VAL ASN SER PHE SER GLY TYR LEU LYS LEU SEQRES 2 A 173 THR ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU SEQRES 3 A 173 GLU ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA SEQRES 4 A 173 ALA ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY SEQRES 5 A 173 ALA LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SEQRES 6 A 173 SER ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL SEQRES 7 A 173 GLY GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS SEQRES 8 A 173 HIS CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY SEQRES 9 A 173 GLU ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE SEQRES 10 A 173 ASN GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA SEQRES 11 A 173 GLY ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL SEQRES 12 A 173 CYS VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL SEQRES 13 A 173 PHE ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE SEQRES 14 A 173 LEU GLU MET LYS SEQRES 1 B 173 GLY HIS MET VAL ASN SER PHE SER GLY TYR LEU LYS LEU SEQRES 2 B 173 THR ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU SEQRES 3 B 173 GLU ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA SEQRES 4 B 173 ALA ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY SEQRES 5 B 173 ALA LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SEQRES 6 B 173 SER ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL SEQRES 7 B 173 GLY GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS SEQRES 8 B 173 HIS CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY SEQRES 9 B 173 GLU ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE SEQRES 10 B 173 ASN GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA SEQRES 11 B 173 GLY ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL SEQRES 12 B 173 CYS VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL SEQRES 13 B 173 PHE ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE SEQRES 14 B 173 LEU GLU MET LYS SEQRES 1 C 173 GLY HIS MET VAL ASN SER PHE SER GLY TYR LEU LYS LEU SEQRES 2 C 173 THR ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU SEQRES 3 C 173 GLU ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA SEQRES 4 C 173 ALA ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY SEQRES 5 C 173 ALA LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SEQRES 6 C 173 SER ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL SEQRES 7 C 173 GLY GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS SEQRES 8 C 173 HIS CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY SEQRES 9 C 173 GLU ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE SEQRES 10 C 173 ASN GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA SEQRES 11 C 173 GLY ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL SEQRES 12 C 173 CYS VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL SEQRES 13 C 173 PHE ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE SEQRES 14 C 173 LEU GLU MET LYS HET U08 A 201 21 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET U08 B 201 21 HET U08 C 201 21 HET EDO C 202 4 HET EDO C 203 4 HETNAM U08 (2~{R},3~{R},4~{S},5~{R})-2-(4-AZANYLPYRROLO[2,1-F][1, HETNAM 2 U08 2,4]TRIAZIN-7-YL)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL) HETNAM 3 U08 OXOLANE-2-CARBONITRILE HETNAM EDO 1,2-ETHANEDIOL HETSYN U08 REMDESIVIR, REACTED FORM HETSYN EDO ETHYLENE GLYCOL FORMUL 4 U08 3(C12 H13 N5 O4) FORMUL 5 EDO 5(C2 H6 O2) FORMUL 12 HOH *148(H2 O) HELIX 1 AA1 ASP A 22 LYS A 31 1 10 HELIX 2 AA2 GLY A 47 THR A 57 1 11 HELIX 3 AA3 ASN A 59 GLY A 73 1 15 HELIX 4 AA4 ASN A 99 GLY A 103 5 5 HELIX 5 AA5 GLN A 107 ASN A 115 1 9 HELIX 6 AA6 PHE A 116 HIS A 119 5 4 HELIX 7 AA7 ALA A 129 GLY A 133 5 5 HELIX 8 AA8 ASP A 135 VAL A 147 1 13 HELIX 9 AA9 ASP A 157 LYS A 172 1 16 HELIX 10 AB1 ASP B 22 LYS B 31 1 10 HELIX 11 AB2 GLY B 47 THR B 57 1 11 HELIX 12 AB3 ASN B 59 GLY B 73 1 15 HELIX 13 AB4 ASN B 99 GLY B 103 5 5 HELIX 14 AB5 GLN B 107 ASN B 115 1 9 HELIX 15 AB6 PHE B 116 HIS B 119 5 4 HELIX 16 AB7 ALA B 129 GLY B 133 5 5 HELIX 17 AB8 ASP B 135 VAL B 147 1 13 HELIX 18 AB9 ASP B 157 GLU B 170 1 14 HELIX 19 AC1 ASP C 22 LYS C 31 1 10 HELIX 20 AC2 GLY C 47 THR C 57 1 11 HELIX 21 AC3 ASN C 59 GLY C 73 1 15 HELIX 22 AC4 ASN C 99 GLY C 103 5 5 HELIX 23 AC5 GLN C 107 ASN C 115 1 9 HELIX 24 AC6 PHE C 116 HIS C 119 5 4 HELIX 25 AC7 ALA C 129 GLY C 133 5 5 HELIX 26 AC8 ASP C 135 VAL C 147 1 13 HELIX 27 AC9 ASP C 157 SER C 166 1 10 SHEET 1 AA1 4 LEU A 10 LYS A 11 0 SHEET 2 AA1 4 VAL A 16 ASN A 20 -1 O ILE A 18 N LEU A 10 SHEET 3 AA1 4 ASN A 150 VAL A 155 1 O LEU A 153 N TYR A 17 SHEET 4 AA1 4 VAL A 121 ALA A 124 1 N ALA A 124 O TYR A 152 SHEET 1 AA2 3 VAL A 34 ALA A 39 0 SHEET 2 AA2 3 HIS A 91 VAL A 96 1 O LEU A 93 N ASN A 37 SHEET 3 AA2 3 SER A 80 SER A 84 -1 N CYS A 81 O HIS A 94 SHEET 1 AA3 4 LEU B 10 LYS B 11 0 SHEET 2 AA3 4 VAL B 16 ASN B 20 -1 O ILE B 18 N LEU B 10 SHEET 3 AA3 4 ASN B 150 VAL B 155 1 O LEU B 153 N TYR B 17 SHEET 4 AA3 4 VAL B 121 ALA B 124 1 N ALA B 124 O TYR B 152 SHEET 1 AA4 3 VAL B 34 ALA B 39 0 SHEET 2 AA4 3 HIS B 91 VAL B 96 1 O VAL B 95 N ASN B 37 SHEET 3 AA4 3 SER B 80 SER B 84 -1 N LEU B 83 O CYS B 92 SHEET 1 AA5 4 LEU C 10 LYS C 11 0 SHEET 2 AA5 4 VAL C 16 ASN C 20 -1 O ILE C 18 N LEU C 10 SHEET 3 AA5 4 ASN C 150 VAL C 155 1 O LEU C 153 N TYR C 17 SHEET 4 AA5 4 VAL C 121 ALA C 124 1 N ALA C 124 O TYR C 152 SHEET 1 AA6 3 VAL C 34 ALA C 39 0 SHEET 2 AA6 3 HIS C 91 VAL C 96 1 O VAL C 95 N ASN C 37 SHEET 3 AA6 3 SER C 80 SER C 84 -1 N LEU C 83 O CYS C 92 SITE 1 AC1 16 ASP A 22 ILE A 23 VAL A 49 GLU A 120 SITE 2 AC1 16 LEU A 126 ALA A 129 ALA A 154 VAL A 155 SITE 3 AC1 16 PHE A 156 ASP A 157 LEU A 160 EDO A 204 SITE 4 AC1 16 HOH A 358 HOH A 361 HOH A 370 MET B 171 SITE 1 AC2 4 TYR A 161 ASP A 162 SER A 166 GLU A 170 SITE 1 AC3 5 ALA A 38 ASN A 40 ALA A 50 HOH A 336 SITE 2 AC3 5 HOH A 357 SITE 1 AC4 4 GLU A 120 GLY A 130 U08 A 201 MET B 171 SITE 1 AC5 13 ASP B 22 ILE B 23 VAL B 49 ALA B 52 SITE 2 AC5 13 GLU B 120 LEU B 126 ALA B 129 ALA B 154 SITE 3 AC5 13 PHE B 156 ASP B 157 LEU B 160 HOH B 314 SITE 4 AC5 13 HOH B 328 SITE 1 AC6 14 ASP C 22 ILE C 23 VAL C 49 GLU C 120 SITE 2 AC6 14 LEU C 126 ALA C 129 GLY C 130 ALA C 154 SITE 3 AC6 14 PHE C 156 ASP C 157 LEU C 160 EDO C 203 SITE 4 AC6 14 HOH C 310 HOH C 314 SITE 1 AC7 5 ASN A 54 LYS A 55 ASN A 59 GLY C 8 SITE 2 AC7 5 TYR C 9 SITE 1 AC8 3 GLY C 130 LEU C 160 U08 C 201 CRYST1 157.238 30.476 111.685 90.00 119.87 90.00 C 1 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 0.006360 0.000000 0.003652 0.00000 SCALE2 0.000000 0.032813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010325 0.00000