Structure of PDB 8pej Chain D Binding Site BS01

Receptor Information

>8pej Chain D (length=539) Species: 498211 (Cellvibrio japonicus Ueda107)

AAPLPELLSNNGKHALMVDGAPYIILGSQTNNSSNYPDALKDVWPSMEKM
GANTLSIPVAWEQIEPVEGQFDFSFVDVLLKEARQRKVRLVLLWFATWKN
NAPHYAPAWVKLDNARFPRVVKEDGDTLNSLSPLGQNTLAADKKAFVELM
KYLAKRDKDHTVIMVQVQNEVGTYGAVRDYSPMAQAVFNAAVPDDLIQKL
QLKPGTWSQVFGRDADEFFHAYQIARYCDEVTVAGKAIKNLPMYVNVALR
NPFNPGLPGQYSSGGGTDNVLHIWKAAAPNIDLIAPDIYFRDYKTVSKVL
ELYTRPDNALFVAEIGNDQPFARYLFPTLGKGGIGFSPFGMDDTDYTNYP
LGAKVYNDETIEQFAQVYRLVNPMMREWARLSYQGQVWGVAEPLDSTTTQ
KIWNAEATPEEKEQHKKDRASALTQQLDLGLWDAEVTYGRPMFWVTPPEG
NTPAAGGALIAQLDDNEYLVTAYKARVEFKPSQELAGKKFMIERVEEGRF
EKGKWVMERVWNGDQTDWGLNFTDRPHLLRVKMASYSVQ

Ligand information

• Ligand ID: YGX
• InChI: InChI=1S/C7H14O6/c8-1-2-3(9)5(11)7(13)6(12)4(2)10/h2-13H,1H2/t2-,3+,4-,5-,6-,7-/m0/s1
• InChIKey: QFYQIWDMMSKNFF-OUIVRQFQSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C(C1C(C(C(C(C1O)O)O)O)O)O
  CACTVS 3.385: OC[CH]1[CH](O)[CH](O)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 2.0.7: C(C1[C@@H]([C@@H](C([C@H]([C@@H]1O)O)O)O)O)O
  CACTVS 3.385: OC[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
• Formula: C7 H14 O6
• Name: (1~{S},2~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol
• PDB chain: 8pej Chain D Residue 605

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pej The development of a broad-spectrum retaining beta-exo-galactosidase activity-based probe.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): N67 K134 N135 N204 E205 E349 F374 N383
• Binding residue (residue number reindexed from 1): N32 K99 N100 N169 E170 E314 F339 N348
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.23: beta-galactosidase.

Gene Ontology

Molecular Function

• GO:0004565 beta-galactosidase activity

Biological Process

• GO:0005975 carbohydrate metabolic process

Cellular Component

• GO:0009341 beta-galactosidase complex

External links

• PDB: RCSB:8pej, PDBe:8pej, PDBj:8pej
• PDBsum: 8pej
• PubMed: 37724332
• UniProt: B3PBE0