Structure of PDB 8dcd Chain A Binding Site BS02

Receptor Information

>8dcd Chain A (length=481) Species: 70601 (Pyrococcus horikoshii OT3)

MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNV
AMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGV
RLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVD
GAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGS
GNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLR
IMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMIT
HWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHR
KGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFG
STCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGA
YKNVDNVVKVVSEAGIAKLVARMRPIGVAKG

Ligand information

• Ligand ID: FRU
• InChI: InChI=1S/C6H12O6/c7-1-3-4(9)5(10)6(11,2-8)12-3/h3-5,7-11H,1-2H2/t3-,4-,5+,6-/m1/s1
• InChIKey: RFSUNEUAIZKAJO-ARQDHWQXSA-N
• SMILES:
  ACDLabs 10.04: OC1C(O)C(OC1(O)CO)CO
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
  CACTVS 3.341: OC[CH]1O[C](O)(CO)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(O1)(CO)O)O)O)O
  CACTVS 3.341: OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O
• Formula: C6 H12 O6
• Name: beta-D-fructofuranose;
  beta-D-fructose;
  D-fructose;
  fructose
• ChEMBL: CHEMBL604608
• ZINC: ZINC000001529270
• PDB chain: 8dcd Chain C Residue 2

Receptor-Ligand Complex Structure

Structure summary

• 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): Y57 K58 D340
• Binding residue (residue number reindexed from 1): Y57 K58 D340
• 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

External links

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