Structure of PDB 8dcd Chain A Binding Site BS04

Receptor Information

>8dcd Chain A (length=481) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNV
AMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGV
RLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVD
GAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGS
GNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLR
IMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMIT
HWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHR
KGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFG
STCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGA
YKNVDNVVKVVSEAGIAKLVARMRPIGVAKG

Ligand information

Ligand ID

InChI

InChI=1S/Zn/q+2

InChIKey

PTFCDOFLOPIGGS-UHFFFAOYSA-N

SMILES

Software	SMILES
CACTVS 3.341	[Zn++]
ACDLabs 10.04 OpenEye OEToolkits 1.5.0	[Zn+2]

Formula

Name

ZINC ION

PDB chain

8dcd Chain A Residue 513 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	8dcd Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
Resolution	2.22 Å
Binding residue (original residue number in PDB)	C98 H234 H329
Binding residue (residue number reindexed from 1)	C98 H234 H329
Annotation score	1

Enzymatic activity

Enzyme Commision number

3.1.-.-
6.5.1.8: 3'-phosphate/5'-hydroxy nucleic acid ligase.

Gene Ontology

	Molecular Function
GO:0008452	RNA ligase activity

	Biological Process
GO:0006396	RNA processing

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Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:8dcd, PDBe:8dcd, PDBj:8dcd
PDBsum	8dcd
PubMed	36130078
UniProt	O59245\|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

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