8Q2B: Adenylate kinase

E. coli Adenylate Kinase variant D158A (AK D158A) showing significant changes to the stacking of catalytic arginine side chains. Determined by X-ray diffraction at 1.76 Å resolution. Released 10 Jul 2024.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Escherichia coli
Chains: 2
Atoms: 3,944
Mol. weight: 49.29 kDa
Ligands: MPO, AP5
Released: 10 Jul 2024

Explore 8Q2B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q2B contains 30 α-helices and 23 β-strands across 2 chains. 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: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
α-helix	13-24	12
β-strand	28-29	2	1
α-helix	31-41	11
α-helix	44-54	11
α-helix	57-60	4
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	113-120	8
β-strand	123-126	4	2
β-strand	131-134	4	2
β-strand	138	1	2
β-strand	142	1	3
β-strand	145	1	3
α-helix	151	1
β-strand	152	1	3
α-helix	153	1
β-strand	154	1	2
α-helix	157-159	3
α-helix	161-170	10
α-helix	171-175	5
α-helix	178-187	10
β-strand	192-197	6	1
α-helix	202-213	12

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	4
α-helix	13-24	12
β-strand	28-30	3	4
α-helix	31-41	11
α-helix	44-54	11
α-helix	57-60	4
α-helix	61-72	12
α-helix	75-77	3
β-strand	81-84	4	4
α-helix	90-98	9
β-strand	105-110	6	4
α-helix	113-115	3
α-helix	116-121	6
β-strand	123-126	4	5
β-strand	131-134	4	5
β-strand	138	1	5
β-strand	145	1	6
α-helix	151	1
β-strand	152	1	6
α-helix	153	1
β-strand	154	1	5
α-helix	161-170	10
α-helix	171-175	5
α-helix	178-187	10
β-strand	192-197	6	4
α-helix	202-213	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenylate kinase	A, B	protein	214	Escherichia coli	P69441 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8Q2B_1 Adenylate kinase (chains A, B)
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI
VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKADQEETVRKRLVEYHQMTAPLIG
YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG

Ligands and cofactors

ID	Name	Formula	Copies
MPO	3[N-morpholino]propane sulfonic acid	C7 H15 N O4 S	1
AP5	Bis(adenosine)-5'-pentaphosphate	C20 H29 N10 O22 P5	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Nam, K., Arattu Thodika, A.R., Grundstrom, C. et al. J Chem Inf Model (2024) 64:150-163. DOI 10.1021/acs.jcim.3c01618 · PubMed

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
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
9L14 1.86 Å, Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate…

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