Structure of PDB 5z19 Chain F Binding Site BS01

Receptor Information
>5z19 Chain F (length=600) Species: 33038 (Mediterraneibacter gnavus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LEYSELYPIQNEYRMMQSLDGMWKFQFDPEEIGKKSGWENGLPAPVSMPV
PSSFADFFTDHKERDYCGDFWYETEFYLPAEWRNKKIWLRFGSITHRGTV
YCNGMEITSHEGGFLPVLADISTVAKPGQVNQVVVKINNELNETSLPCGA
TKILNNGRKLAKPYFDFFNYSGLQRSVWVIALPEESVKDYSVDYELCGTD
ALVKYEVVTTGEHPVIVRLLDAEGELVAETEGKEGILQVANARLWEVRNA
YLYQIVILITDGNGVLDEYREKIGIRTVRIEGTKILLNDRPVYLKGFGKH
EDFPILGRGFHWGIVKRDFECLKWTNANCFRTSHYPYAEEWYQFADEEGF
LIIDEVPAVGMMRSTRNFVAAGSGNYTYFFEALTVPELLKSHIADTEEMI
TRDKNHPSVIAWSLFNEPETITDYAYEYFKEVFAAAETYDFQSRPMTGAF
EKNSKPELCKCYPLCDFICLNRYYGWYISGGPEIEEAEELFRDEMDRWKA
KELNVPFVFTEFGTDTMAGLHKLPSIMWSEEYQKEYLEMNFRVFDSYEFV
QGELAWNFADFQTTEGIMRVDGNHKGVFTRDRQPKAAAVVFKDRWEKKNE
Ligand information
Ligand IDSJ5
InChIInChI=1S/C6H11NO4/c8-4-2-7-1-3(5(4)9)6(10)11/h3-5,7-9H,1-2H2,(H,10,11)/t3-,4+,5+/m0/s1
InChIKeySSMLJUWXZFXWSF-VPENINKCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C1[C@@H]([C@H]([C@@H](CN1)O)O)C(=O)O
CACTVS 3.385O[C@@H]1CNC[C@@H]([C@H]1O)C(O)=O
ACDLabs 12.01C1NCC(C(O)=O)C(C1O)O
OpenEye OEToolkits 2.0.6C1C(C(C(CN1)O)O)C(=O)O
CACTVS 3.385O[CH]1CNC[CH]([CH]1O)C(O)=O
FormulaC6 H11 N O4
Name(3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid
ChEMBLCHEMBL4589187
DrugBank
ZINC
PDB chain5z19 Chain F Residue 701 [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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PDB5z19 Dissection of the substrate preference and structure of gut microbial beta-glucuronidases identifies the major bacteria causing xenobiotic toxicity
Resolution2.503 Å
Binding residue
(original residue number in PDB)		D167 H335 E418 Y474 Y478 E512 W557 K576
Binding residue
(residue number reindexed from 1)		D166 H334 E417 Y473 Y477 E511 W556 K575
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.1.31: beta-glucuronidase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004565 beta-galactosidase activity
GO:0004566 beta-glucuronidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
Biological Process
GO:0005975 carbohydrate metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5z19, PDBe:5z19, PDBj:5z19
PDBsum5z19
PubMed
UniProtQ6W7J7

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