Structure of PDB 6of2 Chain B Binding Site BS01

Receptor Information
>6of2 Chain B (length=528) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MHHSSFQPNNSNFQRKAGGRLVLSTPDVERFVILGNYGVKVHQGEVTIAG
ATLTPIDDVQWVHAPHCHALPVLRTANDTVIELLPCPTAQGLRELARLNP
LFGRLWNETSDTFQIIYTSADAPKRTSLRELASHPAWNKKISELLTSTRR
KPSPILFICGPKSSGKSTFGRLLTNRLMTDRAGHKSRSWKPVMVLDLDPG
QPEFSPPGVVSLTKLRRPNLAPPFCHPGLSFGNEGMTTVRMHAIASVTPA
LDPAHFIACARDLFAYYRRSASQENIPLVVNTPGWIQGTGLDLLAELIAV
LRPTEVLYMSEDGPEETVSALREACASSSTIPFTMLPSQPSWTPATLRSM
AMQSYFHLSPFGPGCEWNPTPLTHLCPWRVRLAGRPDERGVLGIVCYDHQ
YAPELVSDAINGMVMGLVRIEKKEALRGLAVPGDTPLLPLIPNPTGSPLS
PQYTSLVGLVLIRGVSLTASNPELHLLTPVPPSVLHSFRGDELVLVAGKF
DAPTWAYVEGLYWKSNSKDEVPWVEMLH
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain6of2 Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6of2 Cryo-EM reveals active site coordination within a multienzyme pre-rRNA processing complex.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		L239 A240 S271 G273 K274 S275 T276 Q454
Binding residue
(residue number reindexed from 1)		L131 A132 S163 G165 K166 S167 T168 Q339
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0051731 polynucleotide 5'-hydroxyl-kinase activity
Biological Process
GO:0006396 RNA processing

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Molecular Function
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Biological Process
External links
PDB RCSB:6of2, PDBe:6of2, PDBj:6of2
PDBsum6of2
PubMed31488907
UniProtG0S263

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