Structure of PDB 8dcd Chain B

Receptor sequence
>8dcdB (length=481) Species: 70601 (Pyrococcus horikoshii OT3) [Search protein sequence]
MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNV
AMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGV
RLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVD
GAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGS
GNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLR
IMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMIT
HWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHR
KGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFG
STCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGA
YKNVDNVVKVVSEAGIAKLVARMRPIGVAKG
3D structure
PDB8dcd Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
ChainB
Resolution2.22 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 GLC B K17 R23 K17 R23
BS02 FRU B Y57 K58 D340 Y57 K58 D340
BS03 GTP B D95 N202 F204 E206 H234 H329 N330 P378 G379 S380 M381 H404 A406 G407 Y451 K480 D95 N202 F204 E206 H234 H329 N330 P378 G379 S380 M381 H404 A406 G407 Y451 K480
BS04 ZN B C98 H234 H329 C98 H234 H329
BS05 ZN B D95 C98 H203 D95 C98 H203
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:8dcd, PDBe:8dcd, PDBj:8dcd
PDBsum8dcd
PubMed36130078
UniProtO59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)

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