5H2R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphodiesterase
A, B
337Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 3.1.4.-
Find proteins for Q38F42 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q38F42
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
LLN
Query on LLN

Download SDF File 
Download CCD File 
A, 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
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.176 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.756α = 90.00
b = 97.756β = 90.00
c = 120.783γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
BUSTERrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2017-11-01
    Type: Initial release