Structure of PDB 8p1s Chain F Binding Site BS01

Receptor Information

>8p1s Chain F (length=335) Species: 1684 (Bifidobacterium asteroides)

SDTVEWFKQAKYGMMIHWGLYSLLGGEYQGKSSSNYAEWVQSKLQIPNKE
YERLTQAFNPIYFDADAIIDLAKRCGMQYLVVTTKHHDGFAMYRSLVDPY
NVYDATPFHRDVIGELSLACRKAGLRFGLYYSQDLDWHEPDGGGYLSNDI
ETAGTTWDNSWDFTGEKNYDRAFKHKIMPQIEEIMSNYGEISVAWFDVPM
TLSDEQSQTIYDTVKRLQPDCLINSRLGNGRYDYVSLGDNEIPEDSDASD
KVDYNSIEGFKPSKLGLYETAGTINDSWGFAYHDQNWKSPQTIHDYKAHL
NKYGINYLLNVGLDGLGRVPMAAEQALLGARALEA

Ligand information

• Ligand ID: FUC
• InChI: InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3+,4+,5-,6+/m0/s1
• InChIKey: SHZGCJCMOBCMKK-SXUWKVJYSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C
  OpenEye OEToolkits 1.5.0: CC1C(C(C(C(O1)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H]([C@@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
• Formula: C6 H12 O5
• Name: alpha-L-fucopyranose;
  alpha-L-fucose;
  6-deoxy-alpha-L-galactopyranose;
  L-fucose;
  fucose
• ChEMBL: CHEMBL1232862
• DrugBank: DB04473
• ZINC: ZINC000001532814
• PDB chain: 8p1s Chain F Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8p1s Exploring sequence, structure and function of microbial fucosidases from glycoside hydrolase GH29 family
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H38 E59 W60 H107 H108 D218 R247 D260 W305
• Binding residue (residue number reindexed from 1): H17 E38 W39 H86 H87 D197 R226 D239 W278
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0004560 alpha-L-fucosidase activity
• GO:0016787 hydrolase activity

Biological Process

• GO:0006004 fucose metabolic process
• GO:0016139 glycoside catabolic process

Cellular Component

• GO:0005764 lysosome

External links

• PDB: RCSB:8p1s, PDBe:8p1s, PDBj:8p1s
• PDBsum: 8p1s
• UniProt: A0A0F4KU40