5AZI

Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with 4NP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycerol kinase of African human trypanosomes possesses an intrinsic phosphatase activity that can be exploited to accelerate anti-trypanosomal drug design

Balogun, E.O.Inaoka, D.K.Shiba, T.Tokuoka, S.M.Tokumasu, F.Sakamoto, K.Michels, P.A.M.Harada, S.Kita, K.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinase
A, C
518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
Find proteins for D3KVM3 (Trypanosoma brucei gambiense)
Go to UniProtKB:  D3KVM3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glycerol kinase
B, D
518Trypanosoma brucei gambienseMutation(s): 0 
Gene Names: gk
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
4NP
Query on 4NP

Download SDF File 
Download CCD File 
A, C
4-NITROPHENYL PHOSPHATE
C6 H6 N O6 P
XZKIHKMTEMTJQX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
B, D
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.669α = 90.00
b = 120.253β = 89.96
c = 154.593γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release