Structure of PDB 8dcb Chain A Binding Site BS01

Receptor Information

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

MVVPLKRIDKIRWEIPKFDKRMRVPGRVYADEVLLEKMKNDRTLEQATNV
AMLPGIYKYSIVMPDGHQGYGFPIGGVAAFDVKEGVISPGGIGYDINCGV
RLIRTNLTEKEVRPRIKQLVDTLFKNVPSGVGSQGRIKLHWTQIDDVLVD
GAKWAVDNGYGWERDLERLEEGGRMEGADPEAVSQRAKQRGAPQLGSLGS
GNHFLEVQVVDKIFDPEVAKAYGLFEGQVVVMVHTGSRGLGHQVASDYLR
IMERAIRKYRIPWPDRELVSVPFQSEEGQRYFSAMKAAANFAWANRQMIT
HWVRESFQEVFKQDPEGDLGMDIVYDVAHNIGKVEEHEVDGKRVKVIVHR
KGATRAFPPGHEAVPRLYRDVGQPVLIPGSMGTASYILAGTEGAMKETFG
STCHGAGRVLSRKAATRQYRGDRIRQELLNRGIYVRAASMRVVAEEAPGA
YKNVDNVVKVVSEAGIAKLVARMRPIGVAKG

Ligand information

• Ligand ID: GLC
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-DVKNGEFBSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-glucopyranose;
  alpha-D-glucose;
  D-glucose;
  glucose
• ChEMBL: CHEMBL423707
• ZINC: ZINC000003861213
• PDB chain: 8dcb Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dcb Structures of RNA ligase RtcB in complexes with divalent cations and GTP.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): K17 R23
• Binding residue (residue number reindexed from 1): K17 R23
• 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:8dcb, PDBe:8dcb, PDBj:8dcb
• PDBsum: 8dcb
• PubMed: 36130078
• UniProt: O59245|RTCB_PYRHO tRNA-splicing ligase RtcB (Gene Name=rtcB)