Structure of PDB 8v9l Chain x Binding Site BS02

Receptor Information
>8v9l Chain x (length=387) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPHVNIGTIGHVDHGKTTLTAAITKVLHDKFPDLNESRAFDQIDNAPEER
QRGITINISHVEYQTDKRHYAHVDAPGHADYIKNMITGAAQMDGAILVVA
ATDGPMPQTREHVLLARQVGVPYILVALNKSDAVDDEELIELVEMEVREL
LAAQDFDEEAPVVRVSALKALEGDPKWVKSVEELMEAVDASIPDPVRETD
KPFLMPVEDVFTITGRGTVVTGRVERGVINVNEEVEIVGIRPETTKTTVT
GVEMFRKLLDQGQAGDNVGLLLRGIKREDVERGQVVVKPGTTTPHTEFEG
QVYILSKDEGGRHTPFFNNYRPQFYFRTTDVTGVVTLPEGTEMVMPGDNT
DISVKLIQPVAMDEGLRFAIREGGRTVGAGRVTKIIK
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 chain8v9l Chain x 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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PDB8v9l A new family of bacterial ribosome hibernation factors
Resolution3.0 Å
Binding residue
(original residue number in PDB)		D22 H23 G24 K25 T26 T27 N138 K139 S175 L177
Binding residue
(residue number reindexed from 1)		D13 H14 G15 K16 T17 T18 N129 K130 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:8v9l, PDBe:8v9l, PDBj:8v9l
PDBsum8v9l
PubMed38355796
UniProtA0QS98|EFTU_MYCS2 Elongation factor Tu (Gene Name=tuf)

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