HEADER VIRAL PROTEIN, HYDROLASE 28-SEP-20 5RSX TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2 TITLE 2 NSP3 MACRODOMAIN IN COMPLEX WITH ZINC000000388262 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NSP3,PL2-PRO,PAPAIN-LIKE PROTEASE,PAPAIN-LIKE PROTEINASE,PL- COMPND 5 PRO; COMPND 6 EC: 3.4.19.121, 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_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_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS MACRODOMAIN, ADP-RIBOSE, SARS-COV-2, VIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.CORREY,I.D.YOUNG,M.C.THOMPSON,J.S.FRASER REVDAT 5 25-MAY-22 5RSX 1 JRNL REVDAT 4 09-JUN-21 5RSX 1 TITLE REVDAT 3 12-MAY-21 5RSX 1 REMARK REVDAT 2 27-JAN-21 5RSX 1 COMPND REVDAT 1 16-DEC-20 5RSX 0 JRNL AUTH M.SCHULLER,G.J.CORREY,S.GAHBAUER,D.FEARON,T.WU,R.E.DIAZ, JRNL AUTH 2 I.D.YOUNG,L.CARVALHO MARTINS,D.H.SMITH,U.SCHULZE-GAHMEN, JRNL AUTH 3 T.W.OWENS,I.DESHPANDE,G.E.MERZ,A.C.THWIN,J.T.BIEL, JRNL AUTH 4 J.K.PETERS,M.MORITZ,N.HERRERA,H.T.KRATOCHVIL,A.AIMON, JRNL AUTH 5 J.M.BENNETT,J.BRANDAO NETO,A.E.COHEN,A.DIAS,A.DOUANGAMATH, JRNL AUTH 6 L.DUNNETT,O.FEDOROV,M.P.FERLA,M.R.FUCHS,T.J.GORRIE-STONE, JRNL AUTH 7 J.M.HOLTON,M.G.JOHNSON,T.KROJER,G.MEIGS,A.J.POWELL, JRNL AUTH 8 J.G.M.RACK,V.L.RANGEL,S.RUSSI,R.E.SKYNER,C.A.SMITH, JRNL AUTH 9 A.S.SOARES,J.L.WIERMAN,K.ZHU,P.O'BRIEN,N.JURA,A.ASHWORTH, JRNL AUTH10 J.J.IRWIN,M.C.THOMPSON,J.E.GESTWICKI,F.VON DELFT, JRNL AUTH11 B.K.SHOICHET,J.S.FRASER,I.AHEL JRNL TITL FRAGMENT BINDING TO THE NSP3 MACRODOMAIN OF SARS-COV-2 JRNL TITL 2 IDENTIFIED THROUGH CRYSTALLOGRAPHIC SCREENING AND JRNL TITL 3 COMPUTATIONAL DOCKING. JRNL REF SCI ADV V. 7 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 33853786 JRNL DOI 10.1126/SCIADV.ABF8711 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 158969 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 7626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.6000 - 3.1100 0.99 5377 269 0.1583 0.1770 REMARK 3 2 3.1100 - 2.4700 0.98 5160 250 0.1557 0.1692 REMARK 3 3 2.4700 - 2.1600 1.00 5210 285 0.1516 0.1635 REMARK 3 4 2.1600 - 1.9600 1.00 5232 273 0.1533 0.1500 REMARK 3 5 1.9600 - 1.8200 1.00 5189 296 0.1545 0.1703 REMARK 3 6 1.8200 - 1.7100 1.00 5205 255 0.1560 0.1602 REMARK 3 7 1.7100 - 1.6300 0.97 5112 230 0.1508 0.1853 REMARK 3 8 1.6300 - 1.5600 0.97 5033 251 0.1463 0.1683 REMARK 3 9 1.5600 - 1.5000 1.00 5168 286 0.1499 0.1642 REMARK 3 10 1.5000 - 1.4500 1.00 5203 240 0.1526 0.1772 REMARK 3 11 1.4500 - 1.4000 1.00 5187 273 0.1538 0.1719 REMARK 3 12 1.4000 - 1.3600 1.00 5196 241 0.1549 0.1645 REMARK 3 13 1.3600 - 1.3200 1.00 5166 271 0.1588 0.1887 REMARK 3 14 1.3200 - 1.2900 1.00 5183 283 0.1542 0.1685 REMARK 3 15 1.2900 - 1.2600 1.00 5149 270 0.1550 0.1742 REMARK 3 16 1.2600 - 1.2400 1.00 5207 241 0.1582 0.1858 REMARK 3 17 1.2400 - 1.2100 0.93 4839 215 0.1646 0.1749 REMARK 3 18 1.2100 - 1.1900 0.97 5057 264 0.1615 0.1933 REMARK 3 19 1.1900 - 1.1700 0.99 5126 259 0.1660 0.2036 REMARK 3 20 1.1700 - 1.1500 1.00 5138 274 0.1668 0.1894 REMARK 3 21 1.1500 - 1.1300 1.00 5134 250 0.1761 0.1806 REMARK 3 22 1.1300 - 1.1100 1.00 5231 229 0.1831 0.1944 REMARK 3 23 1.1100 - 1.1000 1.00 5125 270 0.1840 0.2202 REMARK 3 24 1.1000 - 1.0800 1.00 5206 245 0.2010 0.2287 REMARK 3 25 1.0800 - 1.0700 1.00 5136 260 0.2165 0.2357 REMARK 3 26 1.0700 - 1.0500 1.00 5154 308 0.2345 0.2663 REMARK 3 27 1.0500 - 1.0400 0.99 5085 262 0.2570 0.2521 REMARK 3 28 1.0400 - 1.0300 0.87 4461 248 0.3087 0.3548 REMARK 3 29 1.0300 - 1.0100 0.79 4094 166 0.3502 0.3868 REMARK 3 30 1.0100 - 1.0000 0.68 3580 162 0.3899 0.3801 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5RSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1001403631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.88557 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.94 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159039 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 6.552 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.73 REMARK 200 R MERGE FOR SHELL (I) : 0.99200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.240 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES, 28% PEG 3000, PH 9.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 19.72200 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 29.58300 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 9.86100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 1 REMARK 465 MET A 2 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 LYS A 29 CG CD CE NZ REMARK 470 LEU A 169 CG CD1 CD2 REMARK 470 LYS B 29 CG CD CE NZ 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 476 O HOH A 482 1.81 REMARK 500 O HOH B 211 O HOH B 292 1.84 REMARK 500 O HOH B 403 O HOH B 419 1.86 REMARK 500 O HOH A 303 O HOH A 357 1.88 REMARK 500 O HOH B 241 O HOH B 392 1.88 REMARK 500 O HOH A 460 O HOH A 501 1.90 REMARK 500 O HOH B 373 O HOH B 425 1.91 REMARK 500 O HOH B 390 O HOH B 404 1.96 REMARK 500 O HOH B 286 O HOH B 416 1.98 REMARK 500 O HOH A 326 O HOH B 213 1.98 REMARK 500 O HOH A 451 O HOH A 481 2.00 REMARK 500 O HOH A 533 O HOH B 372 2.04 REMARK 500 O HOH B 313 O HOH B 405 2.13 REMARK 500 O HOH B 375 O HOH B 440 2.13 REMARK 500 O HOH B 214 O HOH B 373 2.14 REMARK 500 O HOH A 485 O HOH A 500 2.17 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 B 339 O HOH B 384 1554 1.84 REMARK 500 O HOH B 253 O HOH B 256 1556 1.98 REMARK 500 O HOH A 515 O HOH B 399 2455 2.07 REMARK 500 O HOH A 345 O HOH B 248 2455 2.14 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 26 CD GLU A 26 OE2 -0.121 REMARK 500 PRO A 125 N PRO A 125 CA 0.164 REMARK 500 GLU B 26 CD GLU B 26 OE2 -0.085 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 PHE A 116 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 PRO A 125 C - N - CA ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 145 CB - CG - OD2 ANGL. DEV. = -5.6 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 -131.94 54.08 REMARK 500 HIS B 86 -128.97 55.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 552 DISTANCE = 6.04 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YTX A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 202 DBREF 5RSX A 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 DBREF 5RSX B 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 SEQADV 5RSX SER A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSX MET A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSX SER B 1 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSX MET B 2 UNP P0DTD1 EXPRESSION TAG SEQRES 1 A 169 SER MET VAL ASN SER PHE SER GLY TYR LEU LYS LEU THR SEQRES 2 A 169 ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU GLU SEQRES 3 A 169 ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA ALA SEQRES 4 A 169 ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY ALA SEQRES 5 A 169 LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SER SEQRES 6 A 169 ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL GLY SEQRES 7 A 169 GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS HIS SEQRES 8 A 169 CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY GLU SEQRES 9 A 169 ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE ASN SEQRES 10 A 169 GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA GLY SEQRES 11 A 169 ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL CYS SEQRES 12 A 169 VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL PHE SEQRES 13 A 169 ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE LEU SEQRES 1 B 169 SER MET VAL ASN SER PHE SER GLY TYR LEU LYS LEU THR SEQRES 2 B 169 ASP ASN VAL TYR ILE LYS ASN ALA ASP ILE VAL GLU GLU SEQRES 3 B 169 ALA LYS LYS VAL LYS PRO THR VAL VAL VAL ASN ALA ALA SEQRES 4 B 169 ASN VAL TYR LEU LYS HIS GLY GLY GLY VAL ALA GLY ALA SEQRES 5 B 169 LEU ASN LYS ALA THR ASN ASN ALA MET GLN VAL GLU SER SEQRES 6 B 169 ASP ASP TYR ILE ALA THR ASN GLY PRO LEU LYS VAL GLY SEQRES 7 B 169 GLY SER CYS VAL LEU SER GLY HIS ASN LEU ALA LYS HIS SEQRES 8 B 169 CYS LEU HIS VAL VAL GLY PRO ASN VAL ASN LYS GLY GLU SEQRES 9 B 169 ASP ILE GLN LEU LEU LYS SER ALA TYR GLU ASN PHE ASN SEQRES 10 B 169 GLN HIS GLU VAL LEU LEU ALA PRO LEU LEU SER ALA GLY SEQRES 11 B 169 ILE PHE GLY ALA ASP PRO ILE HIS SER LEU ARG VAL CYS SEQRES 12 B 169 VAL ASP THR VAL ARG THR ASN VAL TYR LEU ALA VAL PHE SEQRES 13 B 169 ASP LYS ASN LEU TYR ASP LYS LEU VAL SER SER PHE LEU HET YTX A 201 22 HET DMS A 202 10 HETNAM YTX 2-(3-METHOXY-4-OXIDANYL-PHENYL)ETHANOIC ACID HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 YTX C9 H10 O4 FORMUL 4 DMS C2 H6 O S FORMUL 5 HOH *493(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 PHE A 168 1 12 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 ASP B 105 GLN B 107 5 3 HELIX 15 AB6 LEU B 108 ASN B 115 1 8 HELIX 16 AB7 PHE B 116 HIS B 119 5 4 HELIX 17 AB8 ALA B 129 GLY B 133 5 5 HELIX 18 AB9 ASP B 135 VAL B 147 1 13 HELIX 19 AC1 ASP B 157 LEU B 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 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 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 LEU B 93 N ASN B 37 SHEET 3 AA4 3 SER B 80 SER B 84 -1 N LEU B 83 O CYS B 92 SITE 1 AC1 13 ALA A 38 GLY A 48 VAL A 49 LEU A 126 SITE 2 AC1 13 ALA A 129 GLY A 130 VAL A 155 PHE A 156 SITE 3 AC1 13 ASP A 157 HOH A 327 HOH A 336 HOH A 383 SITE 4 AC1 13 HOH A 404 SITE 1 AC2 6 GLY A 130 ASP A 157 TYR A 161 ASP A 162 SITE 2 AC2 6 HOH A 383 HOH A 406 CRYST1 88.541 88.541 39.444 90.00 90.00 90.00 P 43 8 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 0.011294 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011294 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025352 0.00000