HEADER VIRAL PROTEIN, HYDROLASE 28-SEP-20 5RSI TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF SARS-COV-2 TITLE 2 NSP3 MACRODOMAIN IN COMPLEX WITH ZINC000374420934 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 6 22-MAY-24 5RSI 1 REMARK REVDAT 5 25-MAY-22 5RSI 1 JRNL REVDAT 4 09-JUN-21 5RSI 1 TITLE REVDAT 3 12-MAY-21 5RSI 1 REMARK REVDAT 2 27-JAN-21 5RSI 1 COMPND REVDAT 1 16-DEC-20 5RSI 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. 1.01 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) : 1.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 157843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 7612 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 44.3800 - 3.1400 1.00 5278 258 0.1749 0.1822 REMARK 3 2 3.1400 - 2.4900 1.00 5171 259 0.1804 0.2153 REMARK 3 3 2.4900 - 2.1800 1.00 5102 259 0.1818 0.2005 REMARK 3 4 2.1800 - 1.9800 1.00 5087 277 0.1888 0.1828 REMARK 3 5 1.9800 - 1.8400 1.00 5119 275 0.1873 0.2142 REMARK 3 6 1.8400 - 1.7300 1.00 5073 270 0.1886 0.2000 REMARK 3 7 1.7300 - 1.6400 1.00 5087 219 0.1825 0.2175 REMARK 3 8 1.6400 - 1.5700 1.00 5070 271 0.1762 0.2019 REMARK 3 9 1.5700 - 1.5100 1.00 5053 269 0.1817 0.1964 REMARK 3 10 1.5100 - 1.4600 1.00 5094 238 0.1859 0.1932 REMARK 3 11 1.4600 - 1.4100 1.00 5057 278 0.1900 0.2239 REMARK 3 12 1.4100 - 1.3700 1.00 5139 225 0.1934 0.2460 REMARK 3 13 1.3700 - 1.3400 1.00 5055 263 0.1967 0.2195 REMARK 3 14 1.3400 - 1.3000 1.00 5014 288 0.1999 0.2375 REMARK 3 15 1.3000 - 1.2700 1.00 5048 247 0.2102 0.2496 REMARK 3 16 1.2700 - 1.2500 1.00 5070 244 0.2178 0.2279 REMARK 3 17 1.2500 - 1.2200 1.00 5076 237 0.2160 0.2597 REMARK 3 18 1.2200 - 1.2000 1.00 4997 277 0.2228 0.2643 REMARK 3 19 1.2000 - 1.1800 1.00 5090 259 0.2405 0.2771 REMARK 3 20 1.1800 - 1.1600 1.00 5028 265 0.2505 0.2764 REMARK 3 21 1.1600 - 1.1400 1.00 5095 248 0.2693 0.2891 REMARK 3 22 1.1400 - 1.1200 1.00 5025 219 0.2917 0.3294 REMARK 3 23 1.1200 - 1.1000 1.00 5065 264 0.3118 0.3273 REMARK 3 24 1.1000 - 1.0900 1.00 5035 251 0.3318 0.3301 REMARK 3 25 1.0900 - 1.0700 1.00 5101 253 0.3537 0.3490 REMARK 3 26 1.0700 - 1.0600 1.00 5013 239 0.3639 0.3760 REMARK 3 27 1.0600 - 1.0500 1.00 5041 317 0.3867 0.3946 REMARK 3 28 1.0500 - 1.0300 1.00 4958 270 0.4088 0.4396 REMARK 3 29 1.0300 - 1.0200 0.99 5043 238 0.4582 0.4614 REMARK 3 30 1.0200 - 1.0100 0.62 3147 135 0.5271 0.5250 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.22 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 5RSI 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_1001403616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-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 : ALS REMARK 200 BEAMLINE : 8.3.1 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.94 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 159353 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.010 REMARK 200 RESOLUTION RANGE LOW (A) : 44.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.372 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.02 REMARK 200 R MERGE FOR SHELL (I) : 1.96400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.680 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 (%): 42.24 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 19.65750 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 29.48625 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 9.82875 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 ASP A 157 H TYR A 161 1.44 REMARK 500 O LYS A 158 H ASP A 162 1.56 REMARK 500 O HOH B 370 O HOH B 386 1.82 REMARK 500 O HOH A 321 O HOH B 218 1.92 REMARK 500 O HOH A 433 O HOH A 435 1.96 REMARK 500 O HOH B 374 O HOH B 422 1.99 REMARK 500 O HOH B 344 O HOH B 420 1.99 REMARK 500 O HOH A 452 O HOH A 470 1.99 REMARK 500 O HOH A 373 O HOH A 477 2.07 REMARK 500 OE2 GLU A 25 O HOH A 301 2.11 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 445 O HOH B 391 2454 2.02 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 PRO A 98 N PRO A 98 CA 0.212 REMARK 500 PRO A 125 N PRO A 125 CA 0.195 REMARK 500 ASP A 135 C PRO A 136 N 0.160 REMARK 500 GLU B 26 CD GLU B 26 OE2 -0.076 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 PRO A 98 C - N - CA ANGL. DEV. = 18.6 DEGREES REMARK 500 PRO A 98 CA - N - CD ANGL. DEV. = -10.7 DEGREES REMARK 500 PRO A 125 C - N - CA ANGL. DEV. = 14.7 DEGREES REMARK 500 PRO A 136 C - N - CA ANGL. DEV. = 15.0 DEGREES REMARK 500 PRO A 136 C - N - CD ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG A 141 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 141 NE - CZ - NH2 ANGL. DEV. = 3.7 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 -131.29 53.72 REMARK 500 ASP A 105 117.73 -24.95 REMARK 500 GLN A 107 -18.15 -48.15 REMARK 500 PHE A 156 53.33 -92.27 REMARK 500 SER B 5 72.48 -100.74 REMARK 500 HIS B 86 -125.21 55.77 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 W5D A 201 DBREF 5RSI A 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 DBREF 5RSI B 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 SEQADV 5RSI SER A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSI MET A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSI SER B 1 UNP P0DTD1 EXPRESSION TAG SEQADV 5RSI 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 W5D A 201 34 HETNAM W5D 4-(1,4-OXAZONAN-4-YL)-7H-PYRROLO[2,3-D]PYRIMIDINE FORMUL 3 W5D C13 H18 N4 O FORMUL 4 HOH *425(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 SER A 167 1 11 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 LYS A 19 -1 O ILE A 18 N LEU A 10 SHEET 3 AA1 4 ASN A 150 ALA A 154 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 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 SITE 1 AC1 7 LEU A 10 ASP A 22 ILE A 23 VAL A 49 SITE 2 AC1 7 ALA A 154 PHE A 156 HOH A 359 CRYST1 88.756 88.756 39.315 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 0.011267 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011267 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025436 0.00000