4QNY

Crystal structure of MapK from Leishmania donovani, LDBPK_331470

• PDB DOI: https://doi.org/10.2210/pdb4QNY/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania donovani BPK282A1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-18 Released: 2014-07-09 
• Deposition Author(s): Wernimont, A.K., Loppnau, P., Walker, J.R., Mangos, M., El Bakkouri, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.285 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 

Starting Model: experimental

Literature

Crystal structure of MapK from Leishmania donovani, LDBPK_331470

Wernimont, A.K., Loppnau, P., Walker, J.R., Mangos, M., El Bakkouri, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M.

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.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.01 kDa 
• Atom Count: 5,707 
• Modelled Residue Count: 672 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen activated protein kinase, putative	A, B	354	Leishmania donovani BPK282A1	Mutation(s): 0  Gene Names: LDBK_331470, LDBPK_331470
UniProt
Find proteins for A0A3Q8ITZ9 (Leishmania donovani) Explore A0A3Q8ITZ9  Go to UniProtKB:  A0A3Q8ITZ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.285 
• R-Value Work: 0.234 
• R-Value Observed: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.203	α = 90
b = 86.063	β = 97.34
c = 82.066	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Wernimont, A.K., Loppnau, P., Walker, J.R., Mangos, M., El Bakkouri, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Hui, R., Amani, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description