Structure of PDB 6dsp Chain B Binding Site BS01

Receptor Information

>6dsp Chain B (length=326) Species: 1345695 (Clostridium saccharobutylicum DSM 13864)

VTVTFIPKLTGNAFFESANKGAQKYSEQWGFKVDYEGDANASAASQVSVI
NKAVQQGTNAICLSSVDAAGVKDALKAAADAGVTVTTWDSDVDPSVRKVM
VSQGTPEQLGQMLVQMGYDSLKERGKDPEKDAIKYCWHYSNATVTDQNSW
QVEGEKYIKSKYPNWQNVAPDNYYSNQDAEQAISVGESILSAHSDIDLII
CNDSTALPGQAQAAQNKGLTAKNVTITGFASPNSMKQYCNDGILTRWGLW
DCGIQGAMGCYMAYYIASGNSVKVGDKIEIPTVGTVEVMPNSVLDPKADD
SDTSSGVVLLPERTIFTKDNMNNYDF

Ligand information

• Ligand ID: PAV
• InChI: InChI=1S/C5H10O5/c1-4(7)5(8,9)3(6)2-10-4/h3,6-9H,2H2,1H3/t3-,4+/m0/s1
• InChIKey: BVIYGXUQVXBHQS-IUYQGCFVSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@@]1(C([C@H](CO1)O)(O)O)O
  CACTVS 3.341: C[C]1(O)OC[CH](O)C1(O)O
  CACTVS 3.341: C[C@@]1(O)OC[C@H](O)C1(O)O
  ACDLabs 10.04: OC1(O)C(O)(OCC1O)C
  OpenEye OEToolkits 1.5.0: CC1(C(C(CO1)O)(O)O)O
• Formula: C5 H10 O5
• Name: (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran
• ChEMBL: CHEMBL1235140
• DrugBank: DB04346
• PDB chain: 6dsp Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dsp Identification of novel autoinducer-2 receptors inClostridiareveals plasticity in the binding site of the LsrB receptor family.
• Resolution: 1.37 Å
• Binding residue (original residue number in PDB): K29 F35 F36 D110 D167 Q168 W171 D224 S225 W271
• Binding residue (residue number reindexed from 1): K8 F14 F15 D89 D146 Q147 W150 D203 S204 W250
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.81uM

Gene Ontology

Molecular Function

• GO:0030246 carbohydrate binding

Cellular Component

• GO:0030288 outer membrane-bounded periplasmic space

External links

• PDB: RCSB:6dsp, PDBe:6dsp, PDBj:6dsp
• PDBsum: 6dsp
• PubMed: 30696769
• UniProt: U5MRH9