Brand  (β version)

PDB ID: 5L8Y

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Ligands
Code Name Style Show Link
ZN Zinc ion PoSSuM
MG Magnesium ion PoSSuM
FMT Formic acid PoSSuM
GAI Guanidine PoSSuM
Non-standard Residues
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Glycosylation
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Structure summary

Code : 5L8Y   PDBj   RCSB PDB   PDBe
Header : HYDROLASE
Title : Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-937
Release Data : 2018-03-14
Compound :
mol_id molecule chains
1 Phosphodiesterase A,B
ec: 3.1.4.-
other_details: residues 565-918
Source :
mol_id organism_scientific expression_system
1 Trypanosoma brucei  (taxid:5691) Escherichia coli BL21(DE3)  (taxid:469008)
gene: PDEB1
expression_system_vector_type: Plasmid
expression_system_plasmid: pET28a
Authors : Singh, A.K., Anthonyrajah, E.S., Brown, D.G.
Keywords : parasitic PDE, African Trypanosomiasis, sleeping sickness, hydrolase
Exp. method : X-RAY DIFFRACTION ( 2.14 Å )
Citation :

Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity.

Blaazer, A.R.,Singh, A.K.,de Heuvel, E.  et al.
(2018)  J. Med. Chem.  61 : 3870 - 3888

PubMed: 29672041
DOI: 10.1021/acs.jmedchem.7b01670

Reaction

Chain : A, B
UniProt : Q8WQX9 (Q8WQX9_9TRYP)
Reaction : -
Cofactor: Evidence: Note:
a divalent metal cation ECO:0000256 | RuleBase:RU363067
Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions.