Structure of PDB 6fam Chain A Binding Site BS02

Receptor Information

>6fam Chain A (length=350) Species: 657309 (Bacteroides xylanisolvens XB1A)

NNLGTELDYDTFCFYYDWYGSEAIDGQYRHWAHAIAPDPNGGSGQNPGTI
PGTQESIASNFYPQLGRYSSSDPNILTKHMDMFVMARTGVLALTWWNEQD
ETEAKRIGLILDAADKKKIKVCFHLEPYPSRNVQNLRENIVKLITRYGNH
PAFYRKDGKPLFFIYDSYLIEPSEWEKLLSPGGSITIRNTAYDALMIGLW
TSSPTVQRPFILNAHFDGFYTYFAATGFTYGSTPTNWVSMQKWAKENGKI
FIPSVGPGYIDTRIRPWNGSVIRTRTDGQYYDAMYRKAIEAGVSAISITS
FNEWHEGSQIEPAVPYTSSEFTYLDYENREPDYYLTRTAYWVGKFRESKQ

Ligand information

• Ligand ID: G63
• InChI: InChI=1S/C6H14N2O3/c7-3-1-8-4(2-9)6(11)5(3)10/h3-6,8-11H,1-2,7H2/t3-,4-,5-,6-/m1/s1
• InChIKey: GFTGLZPGRKFGDU-KVTDHHQDSA-N
• SMILES:
  CACTVS 3.385: N[C@@H]1CN[C@H](CO)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 2.0.6: C1[C@H]([C@H]([C@@H]([C@H](N1)CO)O)O)N
  CACTVS 3.385: N[CH]1CN[CH](CO)[CH](O)[CH]1O
  OpenEye OEToolkits 2.0.6: C1C(C(C(C(N1)CO)O)O)N
• Formula: C6 H14 N2 O3
• Name: mannose-alpha-1,3-2-aminodeoxymannojirimycin
• PDB chain: 6fam Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fam Exploration of Strategies for Mechanism-Based Inhibitor Design for Family GH99 endo-alpha-1,2-Mannanases.
• Resolution: 1.13 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
• Binding affinity: PDBbind-CN: -logKd/Ki=4.01,Kd=97.7uM

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:6fam, PDBe:6fam, PDBj:6fam
• PDBsum: 6fam
• PubMed: 29508463
• UniProt: D6D1V7