Structure of PDB 5m77 Chain A Binding Site BS02

Receptor Information

>5m77 Chain A (length=333) Species: 1397 (Niallia circulans)

SDGDTAMKAFNDTFWDPNAKMFWKDSKREKHQDFWVEAELWELVMDAYQH
TSDPALKAELKTQIDDVYDGTVAKYGQDWTNNPFNDDIMWWAMGSARAYQ
ITGNPRYLEAARDHFDFVYDTQWDEEFANGGIWWLNSDHNTKNACINFPA
AQAALYLYDITKDEHYLNAATKIFRWGKTMLTDGNGKVFDRIEIEHGAVP
DATHYNQGTYIGSAVGLYKATGNAVYLDDAVKAAKFTKNHLVDSNGVLNY
EGPNGDLKGGKTILMRNLAHLQKTLDETGQYPEFSAEFDEWLAFNIEMAW
SHQNSDHIVDGNWAGGTYESWSSAAAVQALNGI

Ligand information

• Ligand ID: 7K3
• InChI: InChI=1S/C6H12O5S/c7-1-2-3(8)4(9)5(10)6(12)11-2/h2-10,12H,1H2/t2-,3-,4+,5+,6-/m1/s1
• InChIKey: JUSMHIGDXPKSID-RWOPYEJCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)S)O)O)O)O
  CACTVS 3.385: OC[C@H]1O[C@H](S)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.6: C(C1C(C(C(C(O1)S)O)O)O)O
  CACTVS 3.385: OC[CH]1O[CH](S)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5 S
• Name: 1-thio-alpha-D-mannopyranose;
  (2~{R},3~{S},4~{S},5~{S},6~{R})-2-(hydroxymethyl)-6-sulfanyl-oxane-3,4,5-triol;
  1-thio-alpha-D-mannose;
  1-thio-D-mannose;
  1-thio-mannose
• PDB chain: 5m77 Chain C Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m77 An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.
• Resolution: 1.46 Å
• Binding residue (original residue number in PDB): D228 D239 T241 N292
• Binding residue (residue number reindexed from 1): D190 D201 T203 N254
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.61,Kd=24.7nM

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0030246 carbohydrate binding

Biological Process

• GO:0005975 carbohydrate metabolic process

External links

• PDB: RCSB:5m77, PDBe:5m77, PDBj:5m77
• PDBsum: 5m77
• PubMed: 28766587
• UniProt: Q9Z4P9