5H2R

Crystal structure of T brucei phosphodiesterase B2 bound to compound 15b

• PDB DOI: https://doi.org/10.2210/pdb5H2R/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Mutation(s): No 


• Deposited: 2016-10-17 Released: 2017-11-01 
• Deposition Author(s): Noble, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Trypanosomal Phosphodiesterase B1 and B2 as a Potential Therapy for Human African Trypanosomiasis

Ng, P.S., Noble, C.G., Ng, F.S.B., Chew, S.H., Lim, C.C., Manoharan, V., Wan, K.F., Vachaspati, P., Kaiser, M., Ma, N.L., Gedeck, P., Kounde, C., Rao, S.P.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.21 kDa 
• Atom Count: 6,025 
• Modelled Residue Count: 657 
• Deposited Residue Count: 674 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase	A, B	337	Trypanosoma brucei brucei TREU927	Mutation(s): 0  EC: 3.1.4
UniProt
Find proteins for Q38F42 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38F42  Go to UniProtKB:  Q38F42

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLN	E [auth A], H [auth B]	(4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-(2-hydroxyethyloxy)-3-[2-(2-oxidanylideneimidazolidin-1-yl)ethoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one C28 H38 N4 O5 NSRKPNKUYKBHPD-XZOQPEGZSA-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: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.756	α = 90
b = 97.756	β = 90
c = 120.783	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Noble, C.G.

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description