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

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

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

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| 3D Structure

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CMP (Subject of Investigation/LOI) Query on CMP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C₁₀ H₁₂ N₅ O₆ P IVOMOUWHDPKRLL-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Brown, D.G.

Schroeder, S.

Gil, C.

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

Revision History (Full details and data files)

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