Structure of PDB 5izk Chain B Binding Site BS01

Receptor Information
>5izk Chain B (length=451) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNVNVGVLGHIDSGKTALARALSTTCFSVPLPLLQVTLVDCPGHASLIRT
IIGGAQIIDLMMLVIDVTMQTQSAECLVIGQIACQKLVVVLNKIDLLPEG
KRQAAIDKMTKKMQKTLENTKFRGAPIIPVAAKPGGIPELIELLTSQIST
RDPSGPFLMSVMTGTILSGSISLGDSVEIPALKVVKKVKSMQMFHMPITS
AMQGDRLGICVTQFDPKLLERGLVCAPESLHTVHAALISVEKIPYFRGPL
QTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNFSQEYLFQEQY
LSPRQQWALVEFEKPVTCPRLCLVIGSRCRLAFHGILLHGLEDRNYADSF
LPRLKVYKLKHKHGLVERAMDDYSVIGRSLFKQLFVGLKVHLSTGELGII
DSSGKFKIHIPGGLSPESKKILTPSAERSEPSQHVVLSLTFKRYVFDTHK
R
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 B 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 P94 N146 K147 D149 A186 K187
Binding residue
(residue number reindexed from 1)		G14 K15 T16 A17 P42 N92 K93 D95 A132 K133
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D17 K20 T21 H96
Catalytic site (residue number reindexed from 1) D12 K15 T16 H44
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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