9L14 | pdb_00009l14

Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase

• PDB DOI: https://doi.org/10.2210/pdb9L14/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli HB101, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-13 Released: 2025-06-04 
• Deposition Author(s): Nakamura, I., Amesaka, H., Tanaka, S.I., Matsuo, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Binding mechanism of adenylate kinase-specific monobodies.

Nakamura, I., Amesaka, H., Nagao, S., Orito, N., Negi, S., Tanaka, S.I., Matsuo, T.

(2025) FEBS Lett 599: 1948-1963

• PubMed: 40400134 
• DOI: https://doi.org/10.1002/1873-3468.70076
• Primary Citation Related Structures: 
  9L14


• PubMed Abstract: 
  

  Monobodies are synthetic antibody-mimetic proteins that regulate enzyme functions through protein-protein interactions. In this study, we investigated the binding mechanisms of monobodies to adenylate kinase (Adk). Calorimetric and X-ray crystallographic analyses revealed that CL-1, a monobody specific for the CLOSED form of Adk, binds to the CORE domain of Adk in an enthalpy-driven manner, forming several hydrogen bonds and a cation-π interaction at the protein interface, without perturbing the Adk backbone. In contrast, OP-4, an OPEN-form-specific monobody, exhibited entropy-driven binding. ¹ H- ¹⁵ N 2D nuclear magnetic resonance (NMR), ³¹ P-NMR, and calorimetric studies revealed conformational perturbations to Adk by OP-4, while substrate access remained intact. The different thermodynamic and structural effects between the monobodies highlight the diverse binding mechanisms among monobodies.

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Organizational Affiliation: 
• Division of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara, Japan.
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Japan.
Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute (JASRI), Sayo, Hyogo, Japan.
Faculty of Pharmaceutical Science, Doshisha Women's College of Liberal Arts, Kyo-tanabe, Kyoto, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.1 kDa 
• Atom Count: 2,468 
• Modeled Residue Count: 302 
• Deposited Residue Count: 305 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase	A	214	Escherichia coli K-12	Mutation(s): 0  Gene Names: adk, dnaW, plsA, b0474, JW0463 EC: 2.7.4.3
UniProt
Find proteins for P69441 (Escherichia coli (strain K12)) Explore P69441  Go to UniProtKB:  P69441

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monobody CL-1	B	91	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AP5 (Subject of Investigation/LOI)	C [auth A]	BIS(ADENOSINE)-5'-PENTAPHOSPHATE C20 H29 N10 O22 P5 OIMACDRJUANHTJ-XPWFQUROSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.53	α = 90
b = 63.53	β = 90
c = 128.91	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Nakamura, I., Amesaka, H., Tanaka, S.I., Matsuo, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22K05316

Revision History  

• Version 1.0: 2025-06-04
  Type: Initial release
  
• Version 1.1: 2025-07-30
  Changes: Database references