Structure of PDB 5t62 Chain W Binding Site BS03

Receptor Information
>5t62 Chain W (length=306) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAPFERNIEVW
KQLWRVVERSDLVVQIVDARNPLLFRSVDLERYVKESDKANLLLVNKADL
LTKKQRIAWAKYFISKNISFTFYSALAAAAAAAAAAAAAAAAAAAAAAAA
INIGLVGYPNVGKSSTINSLVGAKKVSVSSTPGKTKHFQTIKLSDSVMLC
DCPGLVFPNFKGELVCNGVLPIDQLRDYIGPAGLVAERIPKYYIEAIYGI
HIQTKDIPTAQELLVAYARARGYMTQGYGSADEPRASRYILKDYVNGKLL
YVNPPP
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain5t62 Chain W Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		S350 T371
Binding residue
(residue number reindexed from 1)		S164 T185
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0000054 ribosomal subunit export from nucleus
GO:0015031 protein transport
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0022625 cytosolic large ribosomal subunit
GO:0043332 mating projection tip

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5t62, PDBe:5t62, PDBj:5t62
PDBsum5t62
PubMed28179369
UniProtP53145|LSG1_YEAST Large subunit GTPase 1 (Gene Name=LSG1)

[Back to BioLiP]