Structure of PDB 4v5s Chain CZ Binding Site BS04

Receptor Information
>4v5s Chain CZ (length=385) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKGEFVRTKPHVNVGTIGHVDHGKTTLTAALTYVAAAENPNVINTAHVEY
ETAKRHYSHVDCPGHADYIKNMITGAAQMDGAILVVSAADGPMPQTREHI
LLARQVGVPYIVVFMNKVDMVDDPELLDLVEMEVRDLLNQYEFPGDEVPV
IRGSALLALEQMHRNPKTRRGENEWVDKIWELLDAIDEYIPTPVRDVDKP
FLMPVEDVFTITGRGTVATGRIERGKVKVGDEVEIVGLAPETRRTVVTGV
EMHRKTLQEGIAGDNVGVLLRGVSREEVERGQVLAKPGSITPHTKFEASV
YVLKKEEGGRHTGFFSGYRPQFYFRTTDVTGVVQLPPGVEMVMPGDNVTF
TVELIKPVALEEGLRFAIREGGRTVGAGVVTKILE
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 chain4v5s Chain CZ Residue 501 [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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PDB4v5s How Mutations in tRNA Distant from the Anticodon Affect the Fidelity of Decoding.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D21 H22 G23 K24 T25 T26 N136 K137 S174 L176
Binding residue
(residue number reindexed from 1)		D21 H22 G23 K24 T25 T26 N116 K117 S154 L156
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
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:4v5s, PDBe:4v5s, PDBj:4v5s
PDBsum4v5s
PubMed21378964
UniProtQ5SHN6|EFTU1_THET8 Elongation factor Tu-A (Gene Name=tufA)

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