Structure of PDB 8odp Chain A

Receptor sequence
>8odpA (length=505) Species: 9606 (Homo sapiens) [Search protein sequence]
MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEEL
RNACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMA
AFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDH
IPVGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRML
QADPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDH
KGQVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIAS
PEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYD
VSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVL
IGGTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLD
KLADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPI
AVIKG
3D structure
PDB8odp Structure of human rtcb archease complex
ChainA
Resolution2.3 Å
3D
structure
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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 MN A C122 H259 H353 C122 H259 H353
BS02 MN A D119 C122 H227 D119 C122 H227
BS03 G2P A D119 N226 H227 Y228 E230 H259 G402 G403 T404 M405 H428 A430 G431 Y475 K504 D119 N226 H227 Y228 E230 H259 G402 G403 T404 M405 H428 A430 G431 Y475 K504
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

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

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