Structure of PDB 5izk Chain A Binding Site BS01

Receptor Information
>5izk Chain A (length=480) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGRRVNVNVGVLGHIDSGKTALARALSTTASTGFSCFSVPLPALLQVTLV
DCPGHASLIRTIIGGAQIIDLMMLVIDVTKGMQTQSAECLVIGQIACQKL
VVVLNKIDLLPEGKRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGP
EAPQGIPELIELLTSQISIPTRDPSGPFLMSVDHCTVMTGTILSGSISLG
DSVEIPALKVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV
CAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSP
APDNFDQEPILDSFNFSQEYLFQEQYLSKHCPRQQWALVEFEKPVTCPRL
CLVIGSRLDATCRLAFHGILLHGLEDRNYADSFLPRLKVYKLKHKHGLVE
RAMDDYSVIGRSLFTNIQLFVGLKVHLSTGELGIIDGKFKIHIPGLSPES
KKISAERSEPSQHVVLSLTFKRYVFDTHKR
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 chain5izk Chain A Residue 1001 [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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PDB5izk Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.
Resolution3.25 Å
Binding residue
(original residue number in PDB)		G19 K20 T21 A22 D149 K187
Binding residue
(residue number reindexed from 1)		G18 K19 T20 A21 D108 K146
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=6.72,Kd=0.19uM
Enzymatic activity
Catalytic site (original residue number in PDB) D17 K20 T21 H96
Catalytic site (residue number reindexed from 1) D16 K19 T20 H55
Enzyme Commision number 3.6.5.-
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0003746 translation elongation factor activity
GO:0003924 GTPase activity
GO:0005525 GTP binding
GO:0016787 hydrolase activity
GO:0035368 selenocysteine insertion sequence binding
GO:0043021 ribonucleoprotein complex binding
Biological Process
GO:0001514 selenocysteine incorporation
GO:0006412 translation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5izk, PDBe:5izk, PDBj:5izk
PDBsum5izk
PubMed27708257
UniProtP57772|SELB_HUMAN Selenocysteine-specific elongation factor (Gene Name=EEFSEC)

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