6EZU | pdb_00006ezu

Schistosoma mansoni Phosphodiesterase 4A

• PDB DOI: https://doi.org/10.2210/pdb6EZU/pdb

• Classification: HYDROLASE
• Organism(s): Schistosoma mansoni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-12-12 
• Deposition Author(s): Brown, D.G., Schroeder, S., Gil, C.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

The structure of Schistosoma mansoni Phosphodiesterase 4A in complex with cAMP

Brown, D.G., Schroeder, S., Gil, C., Munday, J., Koning, H., Siderius, M., Leurs, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 85.73 kDa 
• Atom Count: 5,340 
• Modeled Residue Count: 657 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase	A, B	371	Schistosoma mansoni	Mutation(s): 0  Gene Names: Smp_134140 EC: 3.1.4
UniProt
Find proteins for A0A5K4ENE3 (Schistosoma mansoni) Explore A0A5K4ENE3  Go to UniProtKB:  A0A5K4ENE3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	H [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
CMP (Subject of Investigation/LOI)	E [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.55	α = 90
b = 81.55	β = 90
c = 255.87	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Brown, D.G., Schroeder, S., Gil, C.

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Funding Organization	Location	Grant Number
European Union	United Kingdom	EC-FP7-602666-PDE4NPD

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description