HEADER VIRAL PROTEIN 31-DEC-20 7BF4 TITLE CRYSTAL STRUCTURE OF SARS-COV-2 MACRODOMAIN IN COMPLEX WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: NSP3 MACRODOMAIN; COMPND 3 CHAIN: A; 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: -R3-PRARE2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NSP3, MACRODOMAIN, SARS-COV-2, GMP, GUANOSINE MONOPHOSPHATE, COVID- KEYWDS 2 19, 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 3 31-JAN-24 7BF4 1 REMARK REVDAT 2 07-JUL-21 7BF4 1 JRNL REVDAT 1 13-JAN-21 7BF4 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. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 24080 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1222 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1622 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1285 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.28000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.362 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1439 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1375 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1961 ; 1.686 ; 1.635 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3174 ; 1.549 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 186 ; 6.881 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 59 ;38.670 ;25.593 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 228 ;11.851 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;13.095 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 188 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1623 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 293 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 2 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): -9.8644 22.5887 0.0951 REMARK 3 T TENSOR REMARK 3 T11: 0.0172 T22: 0.0020 REMARK 3 T33: 0.0061 T12: -0.0036 REMARK 3 T13: -0.0068 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.8605 L22: 0.4945 REMARK 3 L33: 0.2501 L12: 0.4390 REMARK 3 L13: -0.1389 L23: -0.2352 REMARK 3 S TENSOR REMARK 3 S11: -0.0009 S12: -0.0087 S13: 0.0304 REMARK 3 S21: -0.0539 S22: 0.0143 S23: 0.0257 REMARK 3 S31: 0.0496 S32: -0.0027 S33: -0.0134 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 : A 163 A 171 REMARK 3 ORIGIN FOR THE GROUP (A): -26.2932 17.5711 9.7243 REMARK 3 T TENSOR REMARK 3 T11: 0.0070 T22: 0.0238 REMARK 3 T33: 0.0363 T12: 0.0004 REMARK 3 T13: -0.0069 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 6.1880 L22: 1.6262 REMARK 3 L33: 6.4464 L12: 0.9356 REMARK 3 L13: 4.9363 L23: 2.6760 REMARK 3 S TENSOR REMARK 3 S11: -0.1499 S12: -0.2064 S13: 0.0469 REMARK 3 S21: -0.0572 S22: -0.0965 S23: 0.1710 REMARK 3 S31: -0.1643 S32: -0.2478 S33: 0.2465 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 7BF4 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_1292113246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUN-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 : X06DA 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 : 25315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 36.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.34900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 47.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2 M SODIUM ACETATE, REMARK 280 0.1 MGCL2, 0.1 M TRIS, PH 8.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 16.67300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.33650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.00950 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 KCAL/MOL 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 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 LYS A 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 MET A 2 CG SD CE 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 304 O HOH A 457 2.03 REMARK 500 O2 EDO A 206 O HOH A 301 2.09 REMARK 500 O HOH A 475 O HOH A 484 2.10 REMARK 500 O1 EDO A 206 O HOH A 302 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 454 O HOH A 480 1556 2.03 REMARK 500 O HOH A 425 O HOH A 480 1556 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 25 CD GLU A 25 OE2 0.079 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 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.1 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 HIS A 86 -128.99 49.69 REMARK 500 THR A 149 -126.18 -102.72 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 5GP 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 EDO A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 210 DBREF 7BF4 A 3 172 UNP P0DTD1 R1AB_SARS2 1025 1194 SEQADV 7BF4 GLY A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF4 HIS A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7BF4 MET A 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 HET 5GP A 201 48 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 EDO A 207 4 HET EDO A 208 4 HET EDO A 209 4 HET EDO A 210 4 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 5GP C10 H14 N5 O8 P FORMUL 3 EDO 9(C2 H6 O2) FORMUL 12 HOH *205(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 GLU A 170 1 14 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 38 0 SHEET 2 AA2 3 HIS A 91 VAL A 95 1 O VAL A 95 N ASN A 37 SHEET 3 AA2 3 SER A 80 SER A 84 -1 N LEU A 83 O CYS A 92 SITE 1 AC1 22 ASN A 40 LYS A 44 GLY A 46 GLY A 47 SITE 2 AC1 22 GLY A 48 ASP A 66 ILE A 69 ALA A 70 SITE 3 AC1 22 ILE A 131 PHE A 132 EDO A 209 HOH A 307 SITE 4 AC1 22 HOH A 318 HOH A 331 HOH A 342 HOH A 347 SITE 5 AC1 22 HOH A 349 HOH A 385 HOH A 388 HOH A 425 SITE 6 AC1 22 HOH A 437 HOH A 454 SITE 1 AC2 6 SER A 7 GLY A 8 TYR A 9 HIS A 86 SITE 2 AC2 6 ALA A 89 HOH A 448 SITE 1 AC3 6 LEU A 12 THR A 13 ASP A 14 GLU A 64 SITE 2 AC3 6 HOH A 378 HOH A 417 SITE 1 AC4 3 GLY A 48 HOH A 334 HOH A 358 SITE 1 AC5 8 ALA A 38 LEU A 126 LEU A 127 SER A 128 SITE 2 AC5 8 ALA A 129 HOH A 302 HOH A 323 HOH A 391 SITE 1 AC6 8 VAL A 49 PRO A 125 VAL A 155 PHE A 156 SITE 2 AC6 8 HOH A 301 HOH A 302 HOH A 327 HOH A 405 SITE 1 AC7 6 ILE A 106 GLN A 107 LYS A 110 HIS A 138 SITE 2 AC7 6 VAL A 142 HOH A 310 SITE 1 AC8 6 ASN A 40 ALA A 70 ASN A 99 PHE A 132 SITE 2 AC8 6 HOH A 398 HOH A 440 SITE 1 AC9 6 TYR A 42 LYS A 44 ASN A 72 5GP A 201 SITE 2 AC9 6 HOH A 315 HOH A 331 SITE 1 AD1 9 TYR A 42 GLY A 46 GLY A 47 GLY A 51 SITE 2 AD1 9 ALA A 52 HOH A 315 HOH A 338 HOH A 339 SITE 3 AD1 9 HOH A 379 CRYST1 72.529 72.529 33.346 90.00 90.00 90.00 P 41 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 0.013788 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013788 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029989 0.00000