Structure of PDB 2dy1 Chain A Binding Site BS02

Receptor Information
>2dy1 Chain A (length=660) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAMIRTVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDYTPEA
KLHRTTVRTGVAPLLFRGHRVFLLDAPGYGDFVGEIRGALEAADAALVAV
SAEAGVQVGTERAWTVAERLGLPRMVVVTKLDKGGDYYALLEDLRSTLGP
ILPIDLPLYEGGKWVGLIDVFHGKAYRYENGEEREAEVPPEERERVQRFR
QEVLEAIVETDEGLLEKYLEGEEVTGEALEKAFHEAVRRGLLYPVALASG
EREIGVLPLLELILEALPSPTERFGDGPPLAKVFKVQVDPFMGQVAYLRL
YRGRLKPGDSLQSEAGQVRLPHLYVPMGKDLLEVEEAEAGFVLGVPKAEG
LHRGMVLWQGEKPESEEVPFARLPDPNVPVALHPKGRTDEARLGEALRKL
LEEDPSLKLERQEETGELLLWGHGELHLATAKERLQDYGVEVEFSVPKVP
YRETIKKVAEGQGKYKKQTGGHGQYGDVWLRLEPASEYGFEWRITGGVIP
SKYQEAIEEGIKEAAKKGVLAGFPVMGFKAIVYNGSYHEVDSSDLAFQIA
ASLAFKKVMAEAHPVLLEPIYRLKVLAPQERVGDVLSDLQARRGRILGME
QEGALSVVHAEVPLAEVLEYYKALPGLTGGAGAYTLEFSHYAEVPPHLAQ
RIVQERAQEG
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 chain2dy1 Chain A Residue 700 [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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PDB2dy1 Crystal structure of EF-G-2 from Thermus thermophilus
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G19 G21 K22 T23 T24 T60 T61 G83 K135 D137 K138 S254 E256
Binding residue
(residue number reindexed from 1)		G14 G16 K17 T18 T19 T55 T56 G78 K130 D132 K133 S249 E251
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
GO:0046872 metal ion 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:2dy1, PDBe:2dy1, PDBj:2dy1
PDBsum2dy1
PubMed
UniProtQ5SI76

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