9L14: Monobody CL-1

Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase. Determined by X-ray diffraction at 1.86 Å resolution. Released 4 Jun 2025.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Escherichia coli (strain K12), synthetic construct
Chains: 2
Atoms: 2,468
Mol. weight: 34.1 kDa
Ligands: AP5, MG
Released: 4 Jun 2025

Explore 9L14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L14 contains 19 α-helices and 18 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, 11 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	44-54	11
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	113-120	8
β-strand	123-126	4	2
β-strand	131-134	4	2
β-strand	138	1	2
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	177-187	11
β-strand	192-197	6	1
α-helix	202-212	11

Chain B: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	4
β-strand	18-23	6	4
α-helix	24-25	2
α-helix	28-29	2
β-strand	31-38	8	5
α-helix	44-45	2
β-strand	46-51	6	5
β-strand	56-59	4	4
α-helix	62-63	2
β-strand	67-75	9	5
β-strand	85-90	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Adenylate kinase	A	protein	214	Escherichia coli (strain K12)	P69441 (AlphaFold model)
Monobody CL-1	B	protein	91	synthetic construct

Sequence of entity 1 (A), FASTA

>9L14_1 Adenylate kinase (chains A)
MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGKQAKDIMDAGKLVT
DELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRI
VGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIG
YYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG

Sequence of entity 2 (B), FASTA

>9L14_2 Monobody CL-1 (chains B)
VSSVPTKLEVVAATPTSLLISWDAPAVTVFYYIITYGETGGNSPVQEFTVPGSKSTATIS
GLSPGVDYTITVYASSGHGRDNSPISINYRT

Ligands and cofactors

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

Primary citation

Binding mechanism of adenylate kinase-specific monobodies. Nakamura, I., Amesaka, H., Nagao, S. et al. FEBS Lett (2025) 599:1948-1963. DOI 10.1002/1873-3468.70076 · 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
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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