9TY2 | pdb_00009ty2

Crystal structure of a Picomolar Nanobody in complex with Maltose Binding Protein, MBP, and maltose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.236 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.162 (DCC) 

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

A Picomolar MBP-Binding Nanobody for Target Enrichment and Modular Complex Engineering.

Chinellato, M.Franzin, E.Vascon, F.Koenig, P.A.Schmidt, F.I.Pontisso, P.Cendron, L.

(2026) ACS Bio Med Chem Au 6: 323-328

  • DOI: https://doi.org/10.1021/acsbiomedchemau.6c00053
  • Primary Citation Related Structures: 
    9TY2

  • PubMed Abstract: 

    The variable domains of heavy chain only antibodies, also called nanobodies, have provided powerful new tools for biomedical research. Their rapid development across multiple fields has helped address emerging scientific and clinical challenges, establishing single-domain antibodies (sdAbs) as highly adaptable platforms for a wide range of biotechnological and therapeutic applications. In this study, we identified a nanobody from an alpaca immune library, sdAbCM1, that binds to the maltose-maltodextrin binding protein, MBP, with picomolar affinity. Biophysical investigations showed that sdAbCM1 recognizes a yet unreported epitope and interacts with MBP in its closed conformation when maltose is present. The high affinity, epitope specificity, and ability to tolerate the ligand-bound state render sdAbCM1 a valuable and versatile biotechnological tool with potential applications such as detection, localization, and purification of MBP fusion proteins and protein complex engineering for single-particle microscopy.


  • Organizational Affiliation
    • Department of Medicine, University of Padova, Via Giustiniani n.2, 35128 Padova (PD), Italy.

Macromolecule Content 

  • Total Structure Weight: 56.89 kDa 
  • Atom Count: 4,197 
  • Modeled Residue Count: 487 
  • Deposited Residue Count: 515 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein387Escherichia coliMutation(s): 0 
Gene Names: malEZ5632ECs5017
UniProt
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Explore P0AEY0 
Go to UniProtKB:  P0AEY0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEY0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody, single fragment heavy chain antibody, NbCM1, sdAbCM1128Vicugna pacosMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G66120GK
GlyCosmos: G66120GK

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.236 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.162 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.602α = 90
b = 52.158β = 92.075
c = 77.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--
Italian Ministry of HealthItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Database references