Structure of PDB 8odo Chain C

Receptor sequence
>8odoC (length=503) Species: 9606 (Homo sapiens) [Search protein sequence]
RSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRN
ACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAF
DMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHIP
VGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQA
DPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKG
QVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASPE
GQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVS
HNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIG
GTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKL
ADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPIAV
IKG
3D structure
PDB8odo Structure of human RTCB in complex with Archease
ChainC
Resolution2.2 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number 6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 5GP C N226 Y228 E230 H259 G402 G403 T404 M405 H428 A430 G431 Y475 K504 N224 Y226 E228 H257 G400 G401 T402 M403 H426 A428 G429 Y473 K502
BS02 MN C C122 H259 H353 C120 H257 H351
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:8odo, PDBe:8odo, PDBj:8odo
PDBsum8odo
PubMed38493148
UniProtQ9Y3I0|RTCB_HUMAN RNA-splicing ligase RtcB homolog (Gene Name=RTCB)

[Back to BioLiP]