HEADER VIRAL PROTEIN 29-APR-20 6YWM TITLE CRYSTAL STRUCTURE OF SARS-COV-2 (COVID-19) NSP3 MACRODOMAIN IN COMPLEX TITLE 2 WITH MES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NSP3 MACRODOMAIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: PP1AB,ORF1AB POLYPROTEIN; COMPND 5 EC: 3.4.19.12,3.4.22.-,3.4.22.69,2.7.7.48,3.6.4.12,3.6.4.13,3.1.13.-, COMPND 6 3.1.-.-,2.1.1.-; 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; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A-TEV KEYWDS NSP3, MACRODOMAIN, ADP-RIBOSE-1"-PHOSPHATASE, ADRP, COVID-19, SARS- KEYWDS 2 COV-2, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 3 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.NI,M.SCHROEDER,V.OLIERIC,E.M.SHARPE,J.A.WOJDYLA,M.WANG,S.KNAPP, AUTHOR 2 A.CHAIKUAD,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 24-JAN-24 6YWM 1 REMARK REVDAT 2 07-JUL-21 6YWM 1 JRNL LINK REVDAT 1 06-MAY-20 6YWM 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. 2.16 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24963 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1263 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) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1844 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : -1.85000 REMARK 3 B33 (A**2) : 0.87000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.276 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.206 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.987 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4019 ; 0.013 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3790 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5425 ; 1.279 ; 1.627 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8807 ; 1.253 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 7.797 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;37.735 ;25.376 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 662 ;14.699 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;18.594 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 509 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4441 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 725 ; 0.002 ; 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 1 169 B 1 169 5272 0.110 0.050 REMARK 3 2 A 1 168 C 1 168 5269 0.100 0.050 REMARK 3 3 B 1 168 C 1 168 5223 0.100 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 1 A 172 REMARK 3 ORIGIN FOR THE GROUP (A): -14.7530 11.6603 -11.6656 REMARK 3 T TENSOR REMARK 3 T11: 0.0965 T22: 0.0069 REMARK 3 T33: 0.0060 T12: 0.0024 REMARK 3 T13: -0.0077 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.9571 L22: 1.0873 REMARK 3 L33: 0.9406 L12: 0.2766 REMARK 3 L13: 0.1066 L23: -0.2978 REMARK 3 S TENSOR REMARK 3 S11: -0.0067 S12: 0.0793 S13: -0.0102 REMARK 3 S21: -0.1142 S22: 0.0343 S23: 0.0741 REMARK 3 S31: -0.0096 S32: 0.0010 S33: -0.0275 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 0 B 169 REMARK 3 ORIGIN FOR THE GROUP (A): -10.6469 30.3038 -40.3192 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.0256 REMARK 3 T33: 0.0167 T12: 0.0130 REMARK 3 T13: 0.0079 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 0.6722 L22: 1.9994 REMARK 3 L33: 1.1490 L12: -0.5199 REMARK 3 L13: 0.4670 L23: -0.2916 REMARK 3 S TENSOR REMARK 3 S11: -0.0115 S12: 0.1043 S13: -0.0248 REMARK 3 S21: 0.1043 S22: 0.0331 S23: 0.0546 REMARK 3 S31: 0.0158 S32: 0.0611 S33: -0.0216 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 1 C 170 REMARK 3 ORIGIN FOR THE GROUP (A): -20.2286 3.8557 16.1104 REMARK 3 T TENSOR REMARK 3 T11: 0.1364 T22: 0.0295 REMARK 3 T33: 0.0358 T12: 0.0601 REMARK 3 T13: 0.0619 T23: 0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.5592 L22: 1.9099 REMARK 3 L33: 1.1035 L12: -0.1375 REMARK 3 L13: 0.3231 L23: -0.5661 REMARK 3 S TENSOR REMARK 3 S11: -0.1439 S12: -0.0476 S13: -0.0728 REMARK 3 S21: 0.2166 S22: 0.1455 S23: 0.1722 REMARK 3 S31: -0.0381 S32: 0.0005 S33: -0.0016 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6YWM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.0 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 : 26281 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 49.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.87300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 6WEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 6000, 0.1M MGCL2, 5% ETHYLENE REMARK 280 GLYCOL, 0.1M MES 6.0, PH 6.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 18.90000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.17900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.52550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.17900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.90000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.52550 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 MET B 171 REMARK 465 LYS B 172 REMARK 465 GLY C 0 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 HIS C 1 CG ND1 CD2 CE1 NE2 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 ASN A 59 5.47 80.90 REMARK 500 HIS A 86 -122.62 53.23 REMARK 500 ASN B 59 2.41 80.99 REMARK 500 HIS B 86 -123.73 51.99 REMARK 500 LEU B 169 51.47 -117.58 REMARK 500 ASN C 59 1.71 82.92 REMARK 500 HIS C 86 -122.47 50.68 REMARK 500 REMARK 500 REMARK: NULL 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 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 OD1 REMARK 620 2 ASP C 157 OD2 65.3 REMARK 620 3 EDO C 203 O2 67.9 2.7 REMARK 620 4 HOH C 306 O 66.5 1.5 1.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 312 O REMARK 620 2 HOH B 325 O 91.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES 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 EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 206 DBREF 6YWM A 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 DBREF 6YWM B 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 DBREF 6YWM C 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 SEQADV 6YWM GLY A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM HIS A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM MET A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM GLY B 0 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM HIS B 1 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM MET B 2 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM GLY C 0 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM HIS C 1 UNP P0DTD1 EXPRESSION TAG SEQADV 6YWM 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 MES A 201 12 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET MG B 201 1 HET EDO B 202 4 HET EDO B 203 4 HET EDO B 204 4 HET MES C 201 12 HET MG C 202 1 HET EDO C 203 4 HET EDO C 204 4 HET EDO C 205 4 HET EDO C 206 4 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 4 MES 2(C6 H13 N O4 S) FORMUL 5 EDO 12(C2 H6 O2) FORMUL 10 MG 2(MG 2+) FORMUL 20 HOH *237(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 ASP A 135 VAL A 147 1 13 HELIX 8 AA8 ASP A 157 MET A 171 1 15 HELIX 9 AA9 ASP B 22 LYS B 31 1 10 HELIX 10 AB1 GLY B 47 THR B 57 1 11 HELIX 11 AB2 ASN B 59 GLY B 73 1 15 HELIX 12 AB3 ASN B 99 GLY B 103 5 5 HELIX 13 AB4 GLN B 107 ASN B 115 1 9 HELIX 14 AB5 PHE B 116 HIS B 119 5 4 HELIX 15 AB6 ALA B 129 GLY B 133 5 5 HELIX 16 AB7 ASP B 135 VAL B 147 1 13 HELIX 17 AB8 ASP B 157 LEU B 169 1 13 HELIX 18 AB9 ASP C 22 LYS C 31 1 10 HELIX 19 AC1 GLY C 47 THR C 57 1 11 HELIX 20 AC2 ASN C 59 GLY C 73 1 15 HELIX 21 AC3 ASN C 99 GLY C 103 5 5 HELIX 22 AC4 GLN C 107 ASN C 115 1 9 HELIX 23 AC5 PHE C 116 HIS C 119 5 4 HELIX 24 AC6 ASP C 135 VAL C 147 1 13 HELIX 25 AC7 ASP C 157 LEU C 169 1 13 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 LEU A 122 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 VAL A 95 N ALA A 39 SHEET 3 AA2 3 SER A 80 SER A 84 -1 N LEU A 83 O CYS A 92 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 VAL B 151 N TYR B 17 SHEET 4 AA3 4 VAL B 121 ALA B 124 1 N LEU B 122 O TYR B 152 SHEET 1 AA4 3 VAL B 34 ALA B 38 0 SHEET 2 AA4 3 HIS B 91 VAL B 95 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 LEU C 122 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 ALA C 39 SHEET 3 AA6 3 SER C 80 SER C 84 -1 N LEU C 83 O CYS C 92 LINK OD1 ASP A 162 MG MG C 202 1555 2354 2.00 LINK MG MG B 201 O HOH B 312 1555 1555 1.91 LINK MG MG B 201 O HOH B 325 1555 1555 2.01 LINK OD2 ASP C 157 MG MG C 202 1555 1555 2.07 LINK MG MG C 202 O2 EDO C 203 1555 1555 2.05 LINK MG MG C 202 O HOH C 306 1555 1555 2.62 SITE 1 AC1 11 ALA A 38 ASN A 40 LYS A 44 SER A 128 SITE 2 AC1 11 ALA A 129 GLY A 130 ILE A 131 PHE A 132 SITE 3 AC1 11 HOH A 325 HOH A 347 HOH A 386 SITE 1 AC2 6 GLU A 114 ASN A 115 HOH A 315 HOH A 346 SITE 2 AC2 6 GLU C 114 ASN C 115 SITE 1 AC3 4 ASN A 117 GLN A 118 HOH A 306 HOH C 352 SITE 1 AC4 3 GLY A 79 SER A 80 ASN A 115 SITE 1 AC5 4 ALA A 134 ASP A 135 HIS A 138 PRO B 74 SITE 1 AC6 3 ILE A 137 ARG A 141 TYR B 42 SITE 1 AC7 5 GLY B 0 HIS B 1 HIS B 91 HOH B 312 SITE 2 AC7 5 HOH B 325 SITE 1 AC8 7 ALA B 21 ASP B 22 ILE B 23 ALA B 154 SITE 2 AC8 7 VAL B 155 PHE B 156 HOH B 328 SITE 1 AC9 3 GLY B 0 HIS B 119 HOH B 353 SITE 1 AD1 3 GLY B 133 ALA B 134 ASP B 135 SITE 1 AD2 10 ALA C 38 ASN C 40 SER C 128 ALA C 129 SITE 2 AD2 10 GLY C 130 ILE C 131 PHE C 132 HOH C 304 SITE 3 AD2 10 HOH C 305 HOH C 318 SITE 1 AD3 5 ASP A 162 HIS C 1 ASP C 157 EDO C 203 SITE 2 AD3 5 HOH C 306 SITE 1 AD4 7 ASP A 162 HIS C 1 MET C 2 ASP C 157 SITE 2 AD4 7 ASN C 159 LEU C 160 MG C 202 SITE 1 AD5 5 HOH A 309 ASN C 117 GLN C 118 GLU C 120 SITE 2 AD5 5 HOH C 326 SITE 1 AD6 4 GLN A 107 LEU A 108 SER A 111 ARG C 148 SITE 1 AD7 5 ALA C 21 ASP C 22 ILE C 23 ALA C 154 SITE 2 AD7 5 PHE C 156 CRYST1 37.800 109.051 114.358 90.00 90.00 90.00 P 21 21 21 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 0.026455 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008744 0.00000