Structure of PDB 7dif Chain A Binding Site BS02

Receptor Information
>7dif Chain A (length=656) Species: 565042 (Bifidobacterium longum subsp. longum JCM 1217) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNVTITSPFWKRRRDQIVESVIPYQWGVMNDEIDTTVPDDPAGNQLADSK
SHAVANLKVAAGELDDEFHGMVFQDSDVYKWLEEAAYALAYHPDPELKAL
CDRTVDLIARAQQSDGYLDTPYQIKSGVWADRPRFSLIQQSHEMYVMGHY
IEAAVAYHQVTGNEQALEVAKKMADCLDANFGPEEGKIHGADGHPEIELA
LAKLYEETGEKRYLTLSQYLIDVRGQDPQFYAKQLKAMNGDNIFHFYKPT
YFQAAEPVRDQQTADGHAVRVGYLCTGVAHVGRLLGDQGLIDTAKRFWKN
IVTRRMYVTGAIGSTHVGESFTYDYDLPNDTMYGETCASVAMSMFAQQML
DLEPKGEYADVLEKELFNGSIAGISLDGKQYYYVNALETTPDGLDNPDRH
HVLSHRVDWFGCACCPANIARLIASVDRYIYTERDGGKTVLSHQFIANTA
EFASGLTVEQRSNFPWDGHVEYTVSLPASATDSSVRFGLRIPGWSRGSYT
LTVNGKPAVGSLEDGFVYLVVNAGDTLEIALELDMSVKFVRANSRVRSDA
GQVAVMRGPLVYCAEQVDNPGDLWNYRLADGVTGADAAVAFQADLLGGVD
TVDLPAVREHADEDDAPLYVDADEPRAGEPATLRLVPYYSWANREIGEMR
VFQRRA
Ligand information
Ligand IDFE0
InChIInChI=1S/C6H12O4/c7-2-3-4(8)1-5(9)6(3)10/h3-10H,1-2H2/t3-,4-,5+,6+/m1/s1
InChIKeyKWAKQXVHPAXYRX-ZXXMMSQZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C1[C@H]([C@H]([C@@H]([C@H]1O)O)CO)O
CACTVS 3.385OC[C@@H]1[C@H](O)C[C@H](O)[C@H]1O
CACTVS 3.385OC[CH]1[CH](O)C[CH](O)[CH]1O
OpenEye OEToolkits 2.0.7C1C(C(C(C1O)O)CO)O
FormulaC6 H12 O4
Name(1S,2S,3R,4R)-3-(hydroxymethyl)cyclopentane-1,2,4-triol
ChEMBL
DrugBank
ZINC
PDB chain7dif Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7dif Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		F73 H142 Y145 H194 H270 V272 E338 C415 C417
Binding residue
(residue number reindexed from 1)		F73 H142 Y145 H194 H267 V269 E335 C412 C414
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.185: non-reducing end beta-L-arabinofuranosidase.
Gene Ontology
Molecular Function
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0046872 metal ion binding
GO:0102478 beta-L-arabinofuranosidase activity
Biological Process
GO:0000272 polysaccharide catabolic process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7dif, PDBe:7dif, PDBj:7dif
PDBsum7dif
PubMed33528085
UniProtE8MGH8|HYBA1_BIFL2 Non-reducing end beta-L-arabinofuranosidase (Gene Name=hypBA1)

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