HEADER VIRAL PROTEIN 17-NOV-20 7KQP TITLE CRYSTAL STRUCTURE OF SARS-COV-2 NSP3 MACRODOMAIN IN COMPLEX WITH ADP- TITLE 2 RIBOSE (P43 CRYSTAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MACRODOMAIN; COMPND 5 SYNONYM: NSP3,PL2-PRO,PAPAIN-LIKE PROTEASE,PAPAIN-LIKE PROTEINASE,PL- COMPND 6 PRO; COMPND 7 EC: 3.4.19.121, 3.4.22.-; COMPND 8 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 KEYWDS MACRODOMAIN, ADP-RIBOSE, SARS-COV-2, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.J.CORREY,I.D.YOUNG,M.C.THOMPSON,J.S.FRASER REVDAT 4 06-MAR-24 7KQP 1 REMARK REVDAT 3 30-JUN-21 7KQP 1 JRNL REVDAT 2 27-JAN-21 7KQP 1 COMPND REVDAT 1 09-DEC-20 7KQP 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. 0.88 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) : 0.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 238989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.108 REMARK 3 R VALUE (WORKING SET) : 0.108 REMARK 3 FREE R VALUE : 0.123 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 11640 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 39.5200 - 2.7300 1.00 7908 393 0.1088 0.1391 REMARK 3 2 2.7300 - 2.1700 1.00 7756 389 0.1037 0.1198 REMARK 3 3 2.1700 - 1.9000 1.00 7685 418 0.1030 0.1133 REMARK 3 4 1.9000 - 1.7200 1.00 7672 410 0.1060 0.1150 REMARK 3 5 1.7200 - 1.6000 1.00 7732 349 0.0983 0.1072 REMARK 3 6 1.6000 - 1.5000 1.00 7649 406 0.0926 0.1048 REMARK 3 7 1.5000 - 1.4300 1.00 7648 380 0.0936 0.0884 REMARK 3 8 1.4300 - 1.3700 1.00 7682 368 0.0939 0.1100 REMARK 3 9 1.3700 - 1.3100 1.00 7644 404 0.0925 0.1087 REMARK 3 10 1.3100 - 1.2700 1.00 7639 407 0.0906 0.1027 REMARK 3 11 1.2700 - 1.2300 1.00 7609 394 0.0864 0.1000 REMARK 3 12 1.2300 - 1.1900 1.00 7628 378 0.0852 0.0996 REMARK 3 13 1.1900 - 1.1600 1.00 7653 382 0.0854 0.1023 REMARK 3 14 1.1600 - 1.1300 1.00 7679 381 0.0838 0.0903 REMARK 3 15 1.1300 - 1.1100 1.00 7673 359 0.0849 0.0969 REMARK 3 16 1.1100 - 1.0900 1.00 7627 398 0.0894 0.1104 REMARK 3 17 1.0900 - 1.0600 1.00 7601 352 0.0954 0.1145 REMARK 3 18 1.0600 - 1.0400 1.00 7576 450 0.1040 0.1238 REMARK 3 19 1.0400 - 1.0200 1.00 7628 394 0.1138 0.1293 REMARK 3 20 1.0200 - 1.0100 1.00 7666 342 0.1265 0.1418 REMARK 3 21 1.0100 - 0.9900 1.00 7653 374 0.1394 0.1578 REMARK 3 22 0.9900 - 0.9800 1.00 7638 395 0.1580 0.1755 REMARK 3 23 0.9800 - 0.9600 1.00 7570 384 0.1642 0.1917 REMARK 3 24 0.9600 - 0.9500 1.00 7564 436 0.1758 0.1895 REMARK 3 25 0.9500 - 0.9400 1.00 7656 409 0.1896 0.1902 REMARK 3 26 0.9400 - 0.9200 1.00 7546 416 0.2103 0.2077 REMARK 3 27 0.9200 - 0.9100 1.00 7564 406 0.2380 0.2442 REMARK 3 28 0.9100 - 0.9000 0.99 7590 389 0.2759 0.2701 REMARK 3 29 0.9000 - 0.8900 0.91 6955 355 0.3161 0.3301 REMARK 3 30 0.8900 - 0.8800 0.83 6258 322 0.3675 0.3836 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) : 10.580 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.84 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 7KQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000253007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.77492 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 : 239545 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.880 REMARK 200 RESOLUTION RANGE LOW (A) : 39.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.386 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.04 REMARK 200 R MERGE FOR SHELL (I) : 1.17600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.920 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: NA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES, 28% PEG 3000, PH 9.5, REMARK 280 VAPOR DIFFUSION, SITTING 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 19.77500 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 29.66250 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 9.88750 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 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 505 O HOH A 530 2.18 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 232 O HOH B 512 4455 1.99 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 LYS A 29 CD - CE - NZ ANGL. DEV. = 26.5 DEGREES REMARK 500 VAL B 144 CG1 - CB - CG2 ANGL. DEV. = 10.7 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 -132.06 55.82 REMARK 500 SER A 128 -1.50 68.63 REMARK 500 SER B 5 58.69 -93.67 REMARK 500 HIS B 86 -128.11 55.74 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 625 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 626 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 627 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 628 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 629 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 630 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH A 631 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH A 632 DISTANCE = 7.03 ANGSTROMS REMARK 525 HOH A 633 DISTANCE = 7.53 ANGSTROMS REMARK 525 HOH B 526 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B 527 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH B 528 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH B 529 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH B 530 DISTANCE = 7.03 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AR6 A 201 DBREF 7KQP A 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 DBREF 7KQP B 3 169 UNP P0DTD1 R1AB_SARS2 1025 1191 SEQADV 7KQP SER A 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7KQP MET A 2 UNP P0DTD1 EXPRESSION TAG SEQADV 7KQP SER B 1 UNP P0DTD1 EXPRESSION TAG SEQADV 7KQP 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 AR6 A 201 57 HETNAM AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY- HETNAM 2 AR6 OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5- HETNAM 3 AR6 TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN HETNAM 4 AR6 PHOSPHATE HETSYN AR6 ADENOSINE-5-DIPHOSPHORIBOSE FORMUL 3 AR6 C15 H23 N5 O14 P2 FORMUL 4 HOH *663(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 SER A 166 1 10 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 ASP B 105 GLN B 107 5 3 HELIX 14 AB5 LEU B 108 ASN B 115 1 8 HELIX 15 AB6 PHE B 116 HIS B 119 5 4 HELIX 16 AB7 ALA B 129 GLY B 133 5 5 HELIX 17 AB8 ASP B 135 VAL B 147 1 13 HELIX 18 AB9 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 39 0 SHEET 2 AA2 3 HIS A 91 VAL A 96 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 32 LEU A 10 ASP A 22 ILE A 23 ALA A 38 SITE 2 AC1 32 ASN A 40 LYS A 44 GLY A 46 GLY A 47 SITE 3 AC1 32 GLY A 48 VAL A 49 ALA A 50 LEU A 126 SITE 4 AC1 32 SER A 128 ALA A 129 GLY A 130 ILE A 131 SITE 5 AC1 32 PHE A 132 ALA A 154 PHE A 156 HOH A 322 SITE 6 AC1 32 HOH A 327 HOH A 342 HOH A 351 HOH A 383 SITE 7 AC1 32 HOH A 400 HOH A 402 HOH A 416 HOH A 427 SITE 8 AC1 32 HOH A 469 HOH A 476 HOH A 479 HOH A 597 CRYST1 88.365 88.365 39.550 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 0.011317 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011317 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025284 0.00000