HEADER HYDROLASE/HYDROLASE INHIBITOR 19-MAY-21 5SAI TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2 TITLE 2 NENDOU IN COMPLEX WITH Z1424343998 COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDYLATE-SPECIFIC ENDORIBONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NENDOU, NON-STRUCTURAL PROTEIN 15, NSP15; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: REP, 1A-1B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, NSP15, KEYWDS 2 NENDOU, SARS-COV-2, SARS, COVID, COVID19, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.S.GODOY,A.DOUANGAMATH,A.M.NAKAMURA,A.DIAS,T.KROJER,G.D.NOSKE, AUTHOR 2 V.O.GAWILJUK,R.S.FERNANDES,M.FAIRHEAD,A.POWELL,L.DUNNET,A.AIMON, AUTHOR 3 D.FEARON,J.BRANDAO-NETO,R.SKYNER,F.VON DELFT,G.OLIVA REVDAT 2 10-MAY-23 5SAI 1 JRNL REVDAT 1 09-JUN-21 5SAI 0 JRNL AUTH A.S.GODOY,A.M.NAKAMURA,A.DOUANGAMATH,Y.SONG,G.D.NOSKE, JRNL AUTH 2 V.O.GAWRILJUK,R.S.FERNANDES,H.D.M.PEREIRA,K.I.Z.OLIVEIRA, JRNL AUTH 3 D.FEARON,A.DIAS,T.KROJER,M.FAIRHEAD,A.POWELL,L.DUNNET, JRNL AUTH 4 J.BRANDAO-NETO,R.SKYNER,R.CHALK,D.BAJUSZ,M.BEGE,A.BORBAS, JRNL AUTH 5 G.M.KESERU,F.VON DELFT,G.OLIVA JRNL TITL ALLOSTERIC REGULATION AND CRYSTALLOGRAPHIC FRAGMENT JRNL TITL 2 SCREENING OF SARS-COV-2 NSP15 ENDORIBONUCLEASE. JRNL REF NUCLEIC ACIDS RES. 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37115000 JRNL DOI 10.1093/NAR/GKAD314 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 (18-SEP-2020) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 129.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 86272 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 4244 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 51 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.59 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1726 REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1662 REMARK 3 BIN R VALUE (WORKING SET) : 0.2277 REMARK 3 BIN FREE R VALUE : 0.2354 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.71 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5500 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 717 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.69430 REMARK 3 B22 (A**2) : 9.69430 REMARK 3 B33 (A**2) : -19.38860 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.400 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.135 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.127 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.129 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.124 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.911 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5646 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7662 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1957 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 960 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5646 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 742 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 5293 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.05 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.44 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 17.45 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 21.4251 -83.7042 11.8620 REMARK 3 T TENSOR REMARK 3 T11: -0.0314 T22: 0.0082 REMARK 3 T33: -0.0955 T12: -0.0315 REMARK 3 T13: 0.0207 T23: 0.0266 REMARK 3 L TENSOR REMARK 3 L11: 0.7099 L22: 0.8277 REMARK 3 L33: 0.4840 L12: 0.2291 REMARK 3 L13: -0.1501 L23: 0.1657 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.0932 S13: -0.0014 REMARK 3 S21: -0.0399 S22: 0.0661 S23: -0.2254 REMARK 3 S31: -0.0085 S32: -0.0590 S33: -0.0364 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 54.5785 -50.8293 3.2157 REMARK 3 T TENSOR REMARK 3 T11: -0.0768 T22: -0.0499 REMARK 3 T33: 0.0124 T12: -0.0161 REMARK 3 T13: 0.0400 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.6262 L22: 0.9915 REMARK 3 L33: 0.5736 L12: 0.2778 REMARK 3 L13: -0.0634 L23: -0.5471 REMARK 3 S TENSOR REMARK 3 S11: 0.1139 S12: -0.0549 S13: -0.0117 REMARK 3 S21: 0.0516 S22: -0.0393 S23: 0.2742 REMARK 3 S31: -0.0692 S32: 0.0474 S33: -0.0746 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5SAI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1001404263. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.91266 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 129.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.27200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 3.33400 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 6X1B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA3 CITRATE PH 5,14% W/V REMARK 280 PEG6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 56.43000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.43000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.43000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 82660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -74.97350 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -129.85791 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 74.97350 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -129.85791 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 74.97350 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -129.85791 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 56.43000 REMARK 350 BIOMT1 5 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 56.43000 REMARK 350 BIOMT1 6 0.500000 -0.866025 0.000000 -74.97350 REMARK 350 BIOMT2 6 0.866025 0.500000 0.000000 -129.85791 REMARK 350 BIOMT3 6 0.000000 0.000000 1.000000 56.43000 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 -2 REMARK 465 GLY B -2 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 717 O HOH A 734 2.17 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 ILE A 27 CA - C - N ANGL. DEV. = -13.6 DEGREES REMARK 500 ASN A 28 C - N - CA ANGL. DEV. = 16.0 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 14 173.75 179.41 REMARK 500 ASN A 28 63.07 33.50 REMARK 500 ASN A 28 -94.86 65.27 REMARK 500 LEU A 248 62.49 64.79 REMARK 500 TYR A 324 -2.71 72.35 REMARK 500 HIS B 14 173.64 179.76 REMARK 500 ASN B 28 63.69 30.59 REMARK 500 ASN B 28 -94.90 63.00 REMARK 500 LEU B 248 62.46 64.74 REMARK 500 TYR B 324 -1.89 71.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 27 12.19 REMARK 500 ILE B 27 11.69 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 ZQM B 401 DBREF 5SAI A 1 346 UNP P0DTD1 R1AB_SARS2 6453 6798 DBREF 5SAI B 1 346 UNP P0DTD1 R1AB_SARS2 6453 6798 SEQADV 5SAI GLY A -2 UNP P0DTD1 EXPRESSION TAG SEQADV 5SAI ALA A -1 UNP P0DTD1 EXPRESSION TAG SEQADV 5SAI MET A 0 UNP P0DTD1 EXPRESSION TAG SEQADV 5SAI GLY B -2 UNP P0DTD1 EXPRESSION TAG SEQADV 5SAI ALA B -1 UNP P0DTD1 EXPRESSION TAG SEQADV 5SAI MET B 0 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 349 GLY ALA MET SER LEU GLU ASN VAL ALA PHE ASN VAL VAL SEQRES 2 A 349 ASN LYS GLY HIS PHE ASP GLY GLN GLN GLY GLU VAL PRO SEQRES 3 A 349 VAL SER ILE ILE ASN ASN THR VAL TYR THR LYS VAL ASP SEQRES 4 A 349 GLY VAL ASP VAL GLU LEU PHE GLU ASN LYS THR THR LEU SEQRES 5 A 349 PRO VAL ASN VAL ALA PHE GLU LEU TRP ALA LYS ARG ASN SEQRES 6 A 349 ILE LYS PRO VAL PRO GLU VAL LYS ILE LEU ASN ASN LEU SEQRES 7 A 349 GLY VAL ASP ILE ALA ALA ASN THR VAL ILE TRP ASP TYR SEQRES 8 A 349 LYS ARG ASP ALA PRO ALA HIS ILE SER THR ILE GLY VAL SEQRES 9 A 349 CYS SER MET THR ASP ILE ALA LYS LYS PRO THR GLU THR SEQRES 10 A 349 ILE CYS ALA PRO LEU THR VAL PHE PHE ASP GLY ARG VAL SEQRES 11 A 349 ASP GLY GLN VAL ASP LEU PHE ARG ASN ALA ARG ASN GLY SEQRES 12 A 349 VAL LEU ILE THR GLU GLY SER VAL LYS GLY LEU GLN PRO SEQRES 13 A 349 SER VAL GLY PRO LYS GLN ALA SER LEU ASN GLY VAL THR SEQRES 14 A 349 LEU ILE GLY GLU ALA VAL LYS THR GLN PHE ASN TYR TYR SEQRES 15 A 349 LYS LYS VAL ASP GLY VAL VAL GLN GLN LEU PRO GLU THR SEQRES 16 A 349 TYR PHE THR GLN SER ARG ASN LEU GLN GLU PHE LYS PRO SEQRES 17 A 349 ARG SER GLN MET GLU ILE ASP PHE LEU GLU LEU ALA MET SEQRES 18 A 349 ASP GLU PHE ILE GLU ARG TYR LYS LEU GLU GLY TYR ALA SEQRES 19 A 349 PHE GLU HIS ILE VAL TYR GLY ASP PHE SER HIS SER GLN SEQRES 20 A 349 LEU GLY GLY LEU HIS LEU LEU ILE GLY LEU ALA LYS ARG SEQRES 21 A 349 PHE LYS GLU SER PRO PHE GLU LEU GLU ASP PHE ILE PRO SEQRES 22 A 349 MET ASP SER THR VAL LYS ASN TYR PHE ILE THR ASP ALA SEQRES 23 A 349 GLN THR GLY SER SER LYS CYS VAL CYS SER VAL ILE ASP SEQRES 24 A 349 LEU LEU LEU ASP ASP PHE VAL GLU ILE ILE LYS SER GLN SEQRES 25 A 349 ASP LEU SER VAL VAL SER LYS VAL VAL LYS VAL THR ILE SEQRES 26 A 349 ASP TYR THR GLU ILE SER PHE MET LEU TRP CYS LYS ASP SEQRES 27 A 349 GLY HIS VAL GLU THR PHE TYR PRO LYS LEU GLN SEQRES 1 B 349 GLY ALA MET SER LEU GLU ASN VAL ALA PHE ASN VAL VAL SEQRES 2 B 349 ASN LYS GLY HIS PHE ASP GLY GLN GLN GLY GLU VAL PRO SEQRES 3 B 349 VAL SER ILE ILE ASN ASN THR VAL TYR THR LYS VAL ASP SEQRES 4 B 349 GLY VAL ASP VAL GLU LEU PHE GLU ASN LYS THR THR LEU SEQRES 5 B 349 PRO VAL ASN VAL ALA PHE GLU LEU TRP ALA LYS ARG ASN SEQRES 6 B 349 ILE LYS PRO VAL PRO GLU VAL LYS ILE LEU ASN ASN LEU SEQRES 7 B 349 GLY VAL ASP ILE ALA ALA ASN THR VAL ILE TRP ASP TYR SEQRES 8 B 349 LYS ARG ASP ALA PRO ALA HIS ILE SER THR ILE GLY VAL SEQRES 9 B 349 CYS SER MET THR ASP ILE ALA LYS LYS PRO THR GLU THR SEQRES 10 B 349 ILE CYS ALA PRO LEU THR VAL PHE PHE ASP GLY ARG VAL SEQRES 11 B 349 ASP GLY GLN VAL ASP LEU PHE ARG ASN ALA ARG ASN GLY SEQRES 12 B 349 VAL LEU ILE THR GLU GLY SER VAL LYS GLY LEU GLN PRO SEQRES 13 B 349 SER VAL GLY PRO LYS GLN ALA SER LEU ASN GLY VAL THR SEQRES 14 B 349 LEU ILE GLY GLU ALA VAL LYS THR GLN PHE ASN TYR TYR SEQRES 15 B 349 LYS LYS VAL ASP GLY VAL VAL GLN GLN LEU PRO GLU THR SEQRES 16 B 349 TYR PHE THR GLN SER ARG ASN LEU GLN GLU PHE LYS PRO SEQRES 17 B 349 ARG SER GLN MET GLU ILE ASP PHE LEU GLU LEU ALA MET SEQRES 18 B 349 ASP GLU PHE ILE GLU ARG TYR LYS LEU GLU GLY TYR ALA SEQRES 19 B 349 PHE GLU HIS ILE VAL TYR GLY ASP PHE SER HIS SER GLN SEQRES 20 B 349 LEU GLY GLY LEU HIS LEU LEU ILE GLY LEU ALA LYS ARG SEQRES 21 B 349 PHE LYS GLU SER PRO PHE GLU LEU GLU ASP PHE ILE PRO SEQRES 22 B 349 MET ASP SER THR VAL LYS ASN TYR PHE ILE THR ASP ALA SEQRES 23 B 349 GLN THR GLY SER SER LYS CYS VAL CYS SER VAL ILE ASP SEQRES 24 B 349 LEU LEU LEU ASP ASP PHE VAL GLU ILE ILE LYS SER GLN SEQRES 25 B 349 ASP LEU SER VAL VAL SER LYS VAL VAL LYS VAL THR ILE SEQRES 26 B 349 ASP TYR THR GLU ILE SER PHE MET LEU TRP CYS LYS ASP SEQRES 27 B 349 GLY HIS VAL GLU THR PHE TYR PRO LYS LEU GLN HET ZQM B 401 14 HETNAM ZQM N-{2-[(PROPAN-2-YL)SULFANYL]PHENYL}UREA FORMUL 3 ZQM C10 H14 N2 O S FORMUL 4 HOH *717(H2 O) HELIX 1 AA1 SER A 1 GLY A 13 1 13 HELIX 2 AA2 PRO A 50 LYS A 60 1 11 HELIX 3 AA3 GLU A 68 LEU A 75 1 8 HELIX 4 AA4 GLU A 113 ALA A 117 5 5 HELIX 5 AA5 GLY A 129 ALA A 137 1 9 HELIX 6 AA6 SER A 207 LEU A 216 1 10 HELIX 7 AA7 ALA A 217 TYR A 225 1 9 HELIX 8 AA8 ALA A 231 VAL A 236 1 6 HELIX 9 AA9 LEU A 250 SER A 261 1 12 HELIX 10 AB1 LEU A 298 SER A 308 1 11 HELIX 11 AB2 SER B 1 GLY B 13 1 13 HELIX 12 AB3 PRO B 50 LYS B 60 1 11 HELIX 13 AB4 GLU B 68 LEU B 75 1 8 HELIX 14 AB5 GLU B 113 ALA B 117 5 5 HELIX 15 AB6 GLY B 129 ASN B 136 1 8 HELIX 16 AB7 SER B 207 LEU B 216 1 10 HELIX 17 AB8 ALA B 217 TYR B 225 1 9 HELIX 18 AB9 ALA B 231 VAL B 236 1 6 HELIX 19 AC1 LEU B 250 SER B 261 1 12 HELIX 20 AC2 LEU B 298 SER B 308 1 11 SHEET 1 AA1 3 VAL A 24 ILE A 27 0 SHEET 2 AA1 3 THR A 30 VAL A 35 -1 O TYR A 32 N SER A 25 SHEET 3 AA1 3 VAL A 38 GLU A 44 -1 O LEU A 42 N VAL A 31 SHEET 1 AA2 5 ILE A 79 ALA A 80 0 SHEET 2 AA2 5 VAL A 121 ASP A 124 1 O PHE A 122 N ILE A 79 SHEET 3 AA2 5 GLY A 140 THR A 144 1 O VAL A 141 N PHE A 123 SHEET 4 AA2 5 ASN A 177 VAL A 182 -1 O ASN A 177 N THR A 144 SHEET 5 AA2 5 SER A 154 VAL A 155 -1 N SER A 154 O TYR A 178 SHEET 1 AA3 5 ILE A 79 ALA A 80 0 SHEET 2 AA3 5 VAL A 121 ASP A 124 1 O PHE A 122 N ILE A 79 SHEET 3 AA3 5 GLY A 140 THR A 144 1 O VAL A 141 N PHE A 123 SHEET 4 AA3 5 ASN A 177 VAL A 182 -1 O ASN A 177 N THR A 144 SHEET 5 AA3 5 VAL A 185 GLN A 187 -1 O GLN A 187 N LYS A 180 SHEET 1 AA4 2 TRP A 86 ASP A 87 0 SHEET 2 AA4 2 ALA A 92 PRO A 93 -1 O ALA A 92 N ASP A 87 SHEET 1 AA5 2 THR A 98 ILE A 99 0 SHEET 2 AA5 2 ASP A 106 ALA A 108 1 O ILE A 107 N THR A 98 SHEET 1 AA6 2 ALA A 160 LEU A 162 0 SHEET 2 AA6 2 VAL A 165 LEU A 167 -1 O VAL A 165 N LEU A 162 SHEET 1 AA7 3 PHE A 263 GLU A 266 0 SHEET 2 AA7 3 VAL A 275 ASP A 282 -1 O PHE A 279 N GLU A 266 SHEET 3 AA7 3 SER A 288 ILE A 295 -1 O VAL A 294 N LYS A 276 SHEET 1 AA8 3 SER A 315 ILE A 322 0 SHEET 2 AA8 3 THR A 325 LYS A 334 -1 O ILE A 327 N VAL A 320 SHEET 3 AA8 3 HIS A 337 PRO A 343 -1 O GLU A 339 N TRP A 332 SHEET 1 AA9 3 VAL B 24 ILE B 27 0 SHEET 2 AA9 3 THR B 30 VAL B 35 -1 O TYR B 32 N SER B 25 SHEET 3 AA9 3 VAL B 38 GLU B 44 -1 O LEU B 42 N VAL B 31 SHEET 1 AB1 5 ILE B 79 ALA B 80 0 SHEET 2 AB1 5 VAL B 121 ASP B 124 1 O PHE B 122 N ILE B 79 SHEET 3 AB1 5 GLY B 140 THR B 144 1 O VAL B 141 N PHE B 123 SHEET 4 AB1 5 ASN B 177 VAL B 182 -1 O LYS B 181 N GLY B 140 SHEET 5 AB1 5 SER B 154 VAL B 155 -1 N SER B 154 O TYR B 178 SHEET 1 AB2 5 ILE B 79 ALA B 80 0 SHEET 2 AB2 5 VAL B 121 ASP B 124 1 O PHE B 122 N ILE B 79 SHEET 3 AB2 5 GLY B 140 THR B 144 1 O VAL B 141 N PHE B 123 SHEET 4 AB2 5 ASN B 177 VAL B 182 -1 O LYS B 181 N GLY B 140 SHEET 5 AB2 5 VAL B 185 VAL B 186 -1 O VAL B 185 N VAL B 182 SHEET 1 AB3 2 TRP B 86 ASP B 87 0 SHEET 2 AB3 2 ALA B 92 PRO B 93 -1 O ALA B 92 N ASP B 87 SHEET 1 AB4 2 THR B 98 ILE B 99 0 SHEET 2 AB4 2 ASP B 106 ALA B 108 1 O ILE B 107 N THR B 98 SHEET 1 AB5 2 ALA B 160 LEU B 162 0 SHEET 2 AB5 2 VAL B 165 LEU B 167 -1 O VAL B 165 N LEU B 162 SHEET 1 AB6 3 PHE B 263 GLU B 266 0 SHEET 2 AB6 3 VAL B 275 ASP B 282 -1 O PHE B 279 N GLU B 266 SHEET 3 AB6 3 SER B 288 ILE B 295 -1 O VAL B 294 N LYS B 276 SHEET 1 AB7 3 SER B 315 ILE B 322 0 SHEET 2 AB7 3 THR B 325 LYS B 334 -1 O ILE B 327 N VAL B 320 SHEET 3 AB7 3 HIS B 337 PRO B 343 -1 O GLU B 339 N TRP B 332 SITE 1 AC1 7 ARG B 135 VAL B 148 LYS B 149 LEU B 151 SITE 2 AC1 7 LYS B 181 VAL B 186 HOH B 512 CRYST1 149.947 149.947 112.860 90.00 90.00 120.00 P 63 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 0.006669 0.003850 0.000000 0.00000 SCALE2 0.000000 0.007701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008861 0.00000