Structure of PDB 5wzr Chain A Binding Site BS02

Receptor Information
>5wzr Chain A (length=630) Species: 1681 (Bifidobacterium bifidum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMQFTMSGTMLRFDETTLRFSFSRDGATWSGCDGIEPQLTREDRSFSFAG
AATVTHERIETGTGVGVRSVFAGFAGADYAFETYIWIERSSGDVLCEWVP
LRECGAEPRIDRVLWPAPLSFDRADAHDVTLITHEQGVMIPNSWPTEVGT
DAVSFGGRFETAGGYMPWFAQLRSDGHAYIAICETPWNAGYDIDHPAGGP
YTHVGMWFEPSLGRMDYRRVVRYRLLDHADHTAICKTYRAYVNERGRLRT
LAEKAARNPSVRDLLGRSWVHVGIKTNVQPDSSFYDPAQPGKNDSLVTFA
QRERQMRTLHEMGAGRLYLHLDGWAQPGYDNGHPDYLPACREAGGWKGMK
SLIDACHEQGDLFGTHDQYRDYYFAARTFDPRNAIRLADGTMPEHAMWAG
GRQTYLCAELAPDYVRRNFSEIATHGIVLDCAYLDVFTCNEGDECSHPEH
RMTRRECYERRAECFEYLLAHGILTSSEEVSDWAVPSLVFCHYAPYDFQM
RSPDAPRHGIPVPLYNLVYHDCVIQPWMMDRVAGGDDYMLYALLNGGAPY
LIRDAAYAGMDGDMNAALRTENDIERCAVVAGLHRRVGMQELVRHDLVGG
DPLVQRSVFADGTAVTCDFHAQTYEVAANG
Ligand information
Ligand IDDJN
InChIInChI=1S/C8H16N2O4/c1-4(12)10-5-2-9-6(3-11)8(14)7(5)13/h5-9,11,13-14H,2-3H2,1H3,(H,10,12)/t5-,6+,7+,8-/m0/s1
InChIKeyGBRAQQUMMCVTAV-OSMVPFSASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(=O)N[C@H]1CN[C@@H]([C@@H]([C@@H]1O)O)CO
CACTVS 3.370CC(=O)N[CH]1CN[CH](CO)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.6CC(=O)NC1CNC(C(C1O)O)CO
CACTVS 3.370CC(=O)N[C@H]1CN[C@H](CO)[C@H](O)[C@@H]1O
ACDLabs 12.01O=C(NC1C(O)C(O)C(NC1)CO)C
FormulaC8 H16 N2 O4
NameN-[(3S,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)piperidin-3-yl]acetamide;
2-acetamido-1,2-dideoxy-D-galacto-nojirimycin;
DGJNAc
ChEMBL
DrugBank
ZINC
PDB chain5wzr Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5wzr The first crystal structure of a family 129 glycoside hydrolase from a probiotic bacterium reveals critical residues and metal cofactors
Resolution2.79 Å
Binding residue
(original residue number in PDB)
Y329 D330 D371 W398 D435 V436 E478 H492 D561
Binding residue
(residue number reindexed from 1)
Y329 D330 D371 W398 D435 V436 E478 H492 D561
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.29,Ki=51nM
Enzymatic activity
Enzyme Commision number 3.2.1.-
Gene Ontology
Molecular Function
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0033926 endo-alpha-N-acetylgalactosaminidase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5wzr, PDBe:5wzr, PDBj:5wzr
PDBsum5wzr
PubMed28546425
UniProtG5ELM1

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