› 8rj4

X-ray diffraction
2.11Å resolution

E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis

Released:
DOI: 10.2210/pdb8rj4/pdb
Model geometry
Fit model/data
PDB entry 8rj4 coloured by chain, front view.
PDB entry 8rj4 coloured by chain, side view.
PDB entry 8rj4 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Magnesium induced structural reorganization in the active site of adenylate kinase.
Nam K, Thodika ARA, Tischlik S, Phoeurk C, Nagy TM, Schierholz L, Ådén J, Rogne P, Drescher M, Sauer-Eriksson AE, Wolf-Watz M
Sci Adv 10 eado5504 (2024)
PMID: 39121211

Function and Biology Details

Reaction catalysed: 
ATP + AMP = 2 ADP
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159587 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Adenylate kinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 214 amino acids
Theoretical weight: 23.62 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P69441 (Residues: 1-214; Coverage: 100%)
Gene names: JW0463, adk, b0474, dnaW, plsA
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand ADP 8 x ADP
Ligand MG 2 x MG
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: MAX IV BEAMLINE BioMAX
Spacegroup: P21
Unit cell:
a: 73.385Å b: 76.29Å c: 93.391Å
α: 90° β: 110.76° γ: 90°
R-values:
R R work R free
0.194 0.191 0.253
Expression system: Escherichia coli

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