Structure of PDB 8dcf Chain A

Receptor sequence
>8dcfA (length=480) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence]
VVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNVA
MLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGVR
LIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVDG
AKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGSG
NHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLRI
MERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMITH
WVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHRK
GATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFGS
TCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGAY
KNVDNVVKVVSEAGIAKLVARMRPIGVAKG
3D structure
PDB8dcf Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
ChainA
Resolution2.42 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.1.-.-
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 FRU A P25 K58 D340 P24 K57 D339
BS02 GTP A D95 C98 N202 F204 E206 H234 P378 G379 S380 M381 A406 G407 Y451 K480 D94 C97 N201 F203 E205 H233 P377 G378 S379 M380 A405 G406 Y450 K479
BS03 CU A C98 H234 H329 C97 H233 H328
BS04 CU A C98 H203 C97 H202
Gene Ontology
Molecular Function
GO:0008452 RNA ligase activity
Biological Process
GO:0006396 RNA processing

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Molecular Function
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Biological Process
External links
PDB RCSB:8dcf, PDBe:8dcf, PDBj:8dcf
PDBsum8dcf
PubMed36130078
UniProtO59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

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