Structure of PDB 8odp Chain E Binding Site BS01

Receptor Information
>8odp Chain E (length=503) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRN
ACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAF
DMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHIP
VGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQA
DPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKG
QVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASPE
GQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVS
HNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIG
GTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKL
ADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPIAV
IKG
Ligand information
Ligand IDMN
InChIInChI=1S/Mn/q+2
InChIKeyWAEMQWOKJMHJLA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mn+2]
CACTVS 3.341[Mn++]
FormulaMn
NameMANGANESE (II) ION
ChEMBL
DrugBankDB06757
ZINC
PDB chain8odp Chain E Residue 601 [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]
PDB8odp Structure of human rtcb archease complex
Resolution2.3 Å
Binding residue
(original residue number in PDB)		C122 H259 H353
Binding residue
(residue number reindexed from 1)		C120 H257 H351
Annotation score1
Enzymatic activity
Enzyme Commision number 6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003972 RNA ligase (ATP) activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008452 RNA ligase activity
GO:0016874 ligase activity
GO:0016886 ligase activity, forming phosphoric ester bonds
GO:0017166 vinculin binding
GO:0046872 metal ion binding
GO:0170057 RNA ligase (GTP) activity
Biological Process
GO:0001701 in utero embryonic development
GO:0001890 placenta development
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0006396 RNA processing
GO:0008033 tRNA processing
Cellular Component
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:0072669 tRNA-splicing ligase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8odp, PDBe:8odp, PDBj:8odp
PDBsum8odp
PubMed38493148
UniProtQ9Y3I0|RTCB_HUMAN RNA-splicing ligase RtcB homolog (Gene Name=RTCB)

[Back to BioLiP]