Structure of PDB 8yk3 Chain B Binding Site BS01

Receptor Information

>8yk3 Chain B (length=619) Species: 398514 (Bifidobacterium bifidum JCM 1254)

GDVVSVADYGAAADSGEDSAPAIIKAVDKAKELAAEGKNVTIAFPKGRYD
IYPDKAERRTLYVSNTVGTNSSYKDKKIGILLEDTKNITVDGQGSDFVFH
GKMTTFAAINSRNVTFKNFSVDFQVPTVIDLTVEKVDAGAKTATVYVPEE
YNYRLSGSNIEWYSDSSPYTGATYWTASNALPYVQLYDTKTGLTVRGDVW
TNPIFQNVTGITDAGNHRLVFSYSSMSDKLANATGISYQMRQTTRDHPGV
FLWKDKDVTLKGIDFRFLHGFGVVGQSTDTITMDGLHFGTGEGTGRSTAG
YADFVQMSGCKGVITVANSSFSNPHDDPINVHGTFLQVVEKISDTKIKVR
YMHNETAGFPSFFVGDQVEFMTKGDMLPVSDSVRTVTAVDGPDGQGGDMG
AGSGSLTDIVLTLDSAIPSAVAVNSHVVENITYTPEVNIHDNVFKETPTR
GILVTTRKKVTIENNLFDGMGMAGIYISNDAQSWYESGPTRDVTIRGNTF
RRSGSDAILVEPTNPTVSTTDTVHKNMTIEGNTFYVNGNRVLNAKSVSDL
TFRDNKIYRENPQVSGSRLFRLNGCKQVVFGGNTYDVGVKAGIDLANMGA
SEVNVSDDSAKVGADGLVP

Ligand information

• Ligand ID: GLA
• InChI: InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6+/m1/s1
• InChIKey: WQZGKKKJIJFFOK-PHYPRBDBSA-N
• SMILES:
  CACTVS 3.341: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)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)O
  CACTVS 3.341: OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)CO
• Formula: C6 H12 O6
• Name: alpha-D-galactopyranose;
  alpha-D-galactose;
  D-galactose;
  galactose;
  ALPHA D-GALACTOSE
• ChEMBL: CHEMBL1233058
• ZINC: ZINC000000901155
• PDB chain: 8yk3 Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8yk3 Crystal Structure of Bifidobacterium bifidum Glycoside Hydrolase Family 110 alpha-Galactosidase Specific for Blood Group B Antigen
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): N90 R270 D351 R475 W509 E511
• Binding residue (residue number reindexed from 1): N65 R245 D326 R450 W484 E486
• Annotation score: 4

External links

• PDB: RCSB:8yk3, PDBe:8yk3, PDBj:8yk3
• PDBsum: 8yk3
• PubMed: 39234034
• UniProt: L8B3G2