8PVW: Short E. coli adenylate kinase

Structure of a short E. coli adenylate kinase in complex with Ap5A. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Feb 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Escherichia coli K-12
Chains: 1
Atoms: 1,616
Mol. weight: 21.46 kDa
Ligands: AP5
Released: 5 Feb 2025

Explore 8PVW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PVW contains 13 α-helices and 5 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
α-helix	13-24	12
β-strand	28-30	3	1
α-helix	31-41	11
α-helix	49-54	6
α-helix	58-60	3
α-helix	61-72	12
α-helix	75-77	3
β-strand	81-84	4	1
α-helix	90-98	9
β-strand	105-110	6	1
α-helix	113-127	15
α-helix	130-132	3
α-helix	134-143	10
α-helix	144-148	5
α-helix	150-160	11
β-strand	165-170	6	1
α-helix	175-186	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenylate kinase	A	protein	187	Escherichia coli K-12	P69441 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PVW_1 Adenylate kinase (chains A)
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI
LKRGETSGRVDDNEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRA
DLEKILG

Ligands and cofactors

ID	Name	Formula	Copies
AP5	Bis(adenosine)-5'-pentaphosphate	C20 H29 N10 O22 P5	1

Primary citation

Structure of a short E. coli adenylate kinase in complex with Ap5A. Rodriguez, J.A., Wolf Watz, M., Nagy, T.M. et al. To be published.

Other PDB entries of the same protein (UniProt P69441 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7APU 1.36 Å, Structure of Adenylate kinase from Escherichia coli in complex with two ADP molecules…
6F7U 1.4 Å, Molecular Mechanism of ATP versus GTP Selectivity of Adenylate Kinase
8CRG 1.49 Å, E. coli adenylate kinase in complex with two ADP molecules as a result of enzymatic AP4A…
8RJ9 1.59 Å, E. coli adenylate kinase Asp84Ala variant in complex with two ADP molecules as a result…
6S36 1.6 Å, Crystal structure of E. coli Adenylate kinase R119K mutant
9R71 1.61 Å, Crystal structure of E. coli Adenylate kinase E114A mutant in complex with inhibitor Ap5a.
6RZE 1.69 Å, Crystal structure of E. coli Adenylate kinase R119A mutant
4X8L 1.7 Å, Crystal structure of E. coli Adenylate kinase P177A mutant in complex with inhibitor Ap5a
8Q2B 1.76 Å, E. coli Adenylate Kinase variant D158A (AK D158A) showing significant changes to the…
9R6U 1.77 Å, Crystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A
1E4V 1.85 Å, Mutant G10V of adenylate kinase from E. coli, modified in the Gly-loop
1E4Y 1.85 Å, Mutant P9L of adenylate kinase from E. coli, modified in the Gly-loop

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