Structure of PDB 4utf Chain A Binding Site BS04

Receptor Information

>4utf Chain A (length=349) Species: 657309 (Bacteroides xylanisolvens XB1A)

NNLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTI
PGTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQD
ETEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNH
PAFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLW
TSSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKI
FIPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITS
FNEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESK

Ligand information

• Ligand ID: IFM
• InChI: InChI=1S/C6H13NO3/c8-3-4-1-7-2-5(9)6(4)10/h4-10H,1-3H2/t4-,5-,6-/m1/s1
• InChIKey: QPYJXFZUIJOGNX-HSUXUTPPSA-N
• SMILES:
  CACTVS 3.341: OC[CH]1CNC[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H]([C@@H](CN1)O)O)CO
  ACDLabs 10.04: OC1C(CO)CNCC1O
  CACTVS 3.341: OC[C@H]1CNC[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1C(C(C(CN1)O)O)CO
• Formula: C6 H13 N O3
• Name: 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE;
  Afegostat;
  isofagomine;
  (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL
• ChEMBL: CHEMBL206468
• DrugBank: DB04545
• ZINC: ZINC000003813668
• PDB chain: 4utf Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4utf Human Gut Bacteroidetes Can Utilize Yeast Mannan Through a Selfish Mechanism.
• Resolution: 1.3 Å
• Binding residue (original residue number in PDB): Y46 W126 H154 E156 Y195 Y252 E333 E336
• Binding residue (residue number reindexed from 1): Y16 W96 H124 E126 Y165 Y222 E303 E306
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.130: glycoprotein endo-alpha-1,2-mannosidase.

Gene Ontology

Molecular Function

• GO:0004559 alpha-mannosidase activity
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:4utf, PDBe:4utf, PDBj:4utf
• PDBsum: 4utf
• PubMed: 25567280
• UniProt: D6D1V7