4NL0 | pdb_00004nl0

Structural and functional characterization of a novel Alpha Kinase in complex with ADP from Entamoeba histolytica

• PDB DOI: https://doi.org/10.2210/pdb4NL0/pdb

• Classification: TRANSFERASE
• Organism(s): Entamoeba histolytica HM-1:IMSS-B
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-13 Released: 2014-11-19 
• Deposition Author(s): Tarique, K.F., Rehman, S.A.A., Bhattacharya, A., Gourinath, S., Mansuri, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of a novel Alpha Kinase in complex with ADP from Entamoeba histolytica

Tarique, K.F., Rehman, S.A.A., Bhattacharya, A., Gourinath, S., Mansuri, M.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 67.59 kDa 
• Atom Count: 4,384 
• Modeled Residue Count: 531 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein kinase, putative	A, B	288	Entamoeba histolytica HM-1:IMSS-B	Mutation(s): 0  Gene Names: EHI8A_073090
UniProt
Find proteins for M3TP73 (Entamoeba histolytica HM-1:IMSS-B) Explore M3TP73  Go to UniProtKB:  M3TP73

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.5	α = 90
b = 90.03	β = 90
c = 123.72	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Tarique, K.F., Rehman, S.A.A., Bhattacharya, A., Gourinath, S., Mansuri, M.S.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary