8RJ6

E. coli adenylate kinase in complex with ATP and AMP and Mg2+ as a result of enzymatic AP4A hydrolysis.

• PDB DOI: https://doi.org/10.2210/pdb8RJ6/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-20 Released: 2024-07-10 
• Deposition Author(s): Tischlik, S., Ronge, P., Wolf-Watz, M., Sauer-Eriksson, A.E.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase.

Abdul Raafik, A.T., Tischlik, S., Nagy, T.M., Phoeurk, C., Schierholtz, L., Aden, J., Rogne, P., Drescher, M., Nam, K., Sauer-Eriksson, S.A., Wolf-Watz, M.

(2024) Sci Adv 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.34 kDa 
• Atom Count: 3,765 
• Modelled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A, B	214	Escherichia coli	Mutation(s): 0  Gene Names: adk, dnaW, plsA, b0474, JW0463 EC: 2.7.4.3
UniProt
Find proteins for P69441 (Escherichia coli (strain K12)) Explore P69441  Go to UniProtKB:  P69441

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	D [auth A], G [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP	E [auth A], H [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.153	α = 90
b = 77.7	β = 94.99
c = 59.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Tischlik, S., Ronge, P., Wolf-Watz, M., Sauer-Eriksson, A.E.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release