Structure of PDB 6dsp Chain A Binding Site BS01

Receptor Information
>6dsp Chain A (length=326) Species: 1345695 (Clostridium saccharobutylicum DSM 13864) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VTVTFIPKLTGNAFFESANKGAQKYSEQWGFKVDYEGDANASAASQVSVI
NKAVQQGTNAICLSSVDAAGVKDALKAAADAGVTVTTWDSDVDPSVRKVM
VSQGTPEQLGQMLVQMGYDSLKERGKDPEKDAIKYCWHYSNATVTDQNSW
QVEGEKYIKSKYPNWQNVAPDNYYSNQDAEQAISVGESILSAHSDIDLII
CNDSTALPGQAQAAQNKGLTAKNVTITGFASPNSMKQYCNDGILTRWGLW
DCGIQGAMGCYMAYYIASGNSVKVGDKIEIPTVGTVEVMPNSVLDPKADD
SDTSSGVVLLPERTIFTKDNMNNYDF
Ligand information
Ligand IDPAV
InChIInChI=1S/C5H10O5/c1-4(7)5(8,9)3(6)2-10-4/h3,6-9H,2H2,1H3/t3-,4+/m0/s1
InChIKeyBVIYGXUQVXBHQS-IUYQGCFVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@]1(C([C@H](CO1)O)(O)O)O
CACTVS 3.341C[C]1(O)OC[CH](O)C1(O)O
CACTVS 3.341C[C@@]1(O)OC[C@H](O)C1(O)O
ACDLabs 10.04OC1(O)C(O)(OCC1O)C
OpenEye OEToolkits 1.5.0CC1(C(C(CO1)O)(O)O)O
FormulaC5 H10 O5
Name(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran
ChEMBLCHEMBL1235140
DrugBankDB04346
ZINC
PDB chain6dsp Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6dsp Identification of novel autoinducer-2 receptors inClostridiareveals plasticity in the binding site of the LsrB receptor family.
Resolution1.37 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 score1
Binding affinityMOAD: Kd=0.81uM
PDBbind-CN: -logKd/Ki=6.09,Kd=0.81uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0030246 carbohydrate binding
Cellular Component
GO:0030288 outer membrane-bounded periplasmic space

View graph for
Molecular Function
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Cellular Component
External links
PDB RCSB:6dsp, PDBe:6dsp, PDBj:6dsp
PDBsum6dsp
PubMed30696769
UniProtU5MRH9

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