Brand  (β version)

PDB ID: 5WQA

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Ligands
Code Name Style Show Link
J20 1-[2-(4-hydroxyphenyl)ethynyl]-9,9-bis(4-methoxyphenyl)-7-oxidanyl-fluorene-2-carbaldehyde PoSSuM
ZN Zinc ion PoSSuM
MG Magnesium ion PoSSuM
Non-standard Residues
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Structure summary

Code : 5WQA   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/INHIBITOR
Title : Crystal structure of PDE4D catalytic domain complexed with Selaginpulvilins K
Release Data : 2017-02-22
Compound :
mol_id molecule chains synonym
1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D A,B DPDE3,PDE43
ec: 3.1.4.53
fragment: UNP residues 381-714
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli BL21  (taxid:511693)
gene: PDE4D, DPDE3
expression_system_strain: BL21
expression_system_vector_type: PLASMID
Authors : Huang, Y., Zhang, T., Zheng, X., Yin, S., Luo, H.B.
Keywords : Natural PDE4 inhibtor, HYDROLASE-INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 2.30 Å )
Citation :

The discovery, complex crystal structure, and recognition mechanism of a novel natural PDE4 inhibitor from Selaginella pulvinata

Huang, Y.,Liu, X.,Wu, D.  et al.
(2017)  Biochem. Pharmacol.  130 : 51 - 59

PubMed: 28159622
DOI: 10.1016/j.bcp.2017.01.016

Reaction

Chain : A, B
UniProt : Q08499 (PDE4D_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
3',5'-cyclic AMP + H2O = AMP + H(+) 3.1.4.53 PubMed:9371713
left-to-right
Cofactor: Evidence: Note:
Zn(2+) ECO:0000269 | PubMed:14609333
ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000269 | PubMed:17582435
Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions.
Mn(2+) ECO:0000269 | PubMed:15260978
ECO:0000269 | PubMed:15576036
ECO:0000250 | UniProtKB:Q07343
Binds 2 divalent metal cations per subunit (PubMed:15260978, PubMed:15576036). Site 2 has a preference for magnesium and/or manganese ions (By similarity).