5GN6

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of trypanocidal coumarins with dual-inhibition for African trypanosomes glycerol kinase and alternative oxidase

Balogun, E.O.Inaoka, D.K.Shiba, T.Tsuge, T.May, B.Sato, T.Kido, Y.Takeshi, N.Aoki, T.Honma, T.Tanaka, A.Inoue, M.Matsuoka, S.Michels, P.A.M.Watanabe, Y.Moore, A.L.Harada, S.Kita, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinase
A, B, C, D
514Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
EC: 2.7.1.30
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Go to UniProtKB:  D3KVM3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6Y0
Query on 6Y0

Download SDF File 
Download CCD File 
A, B, C, D
4-butyl-7,8-bis(oxidanyl)chromen-2-one
C13 H14 O4
GDGBIWNBPUQGGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.424α = 90.00
b = 122.040β = 90.00
c = 154.735γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Data collection