Structure of PDB 5w75 Chain D Binding Site BS02

Receptor Information
>5w75 Chain D (length=387) Species: 309803 (Thermotoga neapolitana DSM 4359) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKPHVNVGTIGHVDHGKSTLTAAITKYLSLKGLAQYVPYDQIDKAPEEKA
RGITINITHVEYETEKRHYAHIDCPGHADYIKNMITGAAQMDGAILVVAA
TDGPMPQTREHVLLARQVGVPYMIVFINKTDMVDDPELIELVEMEVRDLL
SQYEYPGDEVPVIKGSALKALEANHEAYKPIQELLDAMDNYIPDPQRDVD
KPFLMPIEDVFSITGRGTVVTGRIERGRIRPGDEVEIIGLSEIRKTVVTS
VEMFRKELDEGIAGDNVGCLLRGIDKDEVERGQVLAAPGSIKPHKRFKAE
VYVLKKEEGGRHTPFFKGYKPQFYIRTTDVTGEIVLPEGVEMVMPGDHVE
MEIELIYPVAIEKGQRFAIREGGRTVGAGVVTEVIEL
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain5w75 Chain D Residue 401 [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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PDB5w75 Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.
Resolution2.298 Å
Binding residue
(original residue number in PDB)		V21 D22 G24 K25 S26 T27 Y47 N136 K137 D139 S174 L176
Binding residue
(residue number reindexed from 1)		V13 D14 G16 K17 S18 T19 Y39 N128 K129 D131 S166 L168
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:0006412 translation
GO:0006414 translational elongation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5w75, PDBe:5w75, PDBj:5w75
PDBsum5w75
PubMed29276038
UniProtB9K884|EFTU_THENN Elongation factor Tu (Gene Name=tuf)

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