5KB5 | pdb_00005kb5

Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate

• PDB DOI: https://doi.org/10.2210/pdb5KB5/pdb

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


• Deposited: 2016-06-02 Released: 2017-06-07 
• Deposition Author(s): Oliveira, R.R., Neto, R.M., Polo, C.C., Tonoli, C.C.C., Murakami, M.T., Franchini, K.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the adenosine kinase from Mus musculus in complex with adenosine and adenosine-diphosphate

Oliveira, R.R., Neto, R.M., Polo, C.C., Tonoli, C.C.C., Murakami, M.T., Franchini, K.G.

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)

Macromolecule Content 

• Total Structure Weight: 42.03 kDa 
• Atom Count: 2,903 
• Modeled Residue Count: 341 
• Deposited Residue Count: 363 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine kinase	A	363	Mus musculus	Mutation(s): 0  Gene Names: Adk EC: 2.7.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for P55264 (Mus musculus) Explore P55264  Go to UniProtKB:  P55264
IMPC:  MGI:87930

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ADN	B [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
PG4	H [auth A], I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	J [auth A], K [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.264	α = 90
b = 73.559	β = 90
c = 84.33	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Oliveira, R.R., Neto, R.M., Polo, C.C., Tonoli, C.C.C., Murakami, M.T., Franchini, K.G.

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description