Structure of PDB 8dmf Chain A Binding Site BS02

Receptor Information
>8dmf Chain A (length=718) Species: 226186 (Bacteroides thetaiotaomicron VPI-5482) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVYQTNEIKNIALLGSSGSGKTTLVEAMLFESGVIKRRGSVAAKNTVSD
YFPVEQEYGYSVFSTVLHVEWNNKKLNIIDCPGSDDFVGSTVTALNVTDT
AIILLNGQYGVEVGTQNHFRYTEKLNKPVIFLVNQLDNEKCDYDNILEQL
KEAYGSKVVPIQYPIATGPGFNALIDVLLMKKYSWKPEGGAPVIEDIPAE
EMDKAMEMHKALVEAAAENDEGLMEKFFEQDSLTEDEMREGIRKGLIARG
MFPVFCVCGGKDMGVRRLMEFLGNVVPFVSEMPKVENTDGKEVAPDVNGP
ESLYFFKTSVEPHIGEVSYFKVMSGKVREGDDLLNADRGSKERIAQIYVV
AGGNRVKVEELQAGDIGAAVKLKDVKTGNTLNGKDCDYKFNFIKYPNSKY
SRAIKPVNEADVEKMMTILNRMREEDPTWVIEQSKELKQTLVHGQGEFHL
RTLKWRLENNEKLQVKFEEPKIPYRETITKAARADYRHKKQSGGAGQFGE
VHLIVEPYKEGMPVPDTYKFNGQEFKITVRGTEEIPLEWGGKLVFINSIV
GGSIDARFLPAIMKGIMSRLEQGPLTGSYARDVRVIVYDGKMHPVDSNEI
SFMLAGRNAFSEAFKNAGPKILEPIYDVEVFVPSDRMGDVMGDLQGRRAM
IMGMSSEKGFEKLVAKVPLKEMSSYSTALSSLTGGRASFIMKFASYELVP
TDVQDKLIKDFEAKQTEE
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain8dmf Chain A Residue 802 [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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PDB8dmf Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		S18 G19 G21 K22 T23 T24 Y60 S61 Q135 D137 G259 G260
Binding residue
(residue number reindexed from 1)		S18 G19 G21 K22 T23 T24 Y60 S61 Q135 D137 G259 G260
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
Biological Process
GO:0006414 translational elongation
GO:0032790 ribosome disassembly

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8dmf, PDBe:8dmf, PDBj:8dmf
PDBsum8dmf
PubMed36472247
UniProtQ8A5S1

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