9B0A | pdb_00009b0a

GA10 nanobody bound to 2C7 peptide mimitope of Neisseria gonorrhoeae lipooligosaccharide

• PDB DOI: https://doi.org/10.2210/pdb9B0A/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): synthetic construct
• Expression System: Escherichia coli MC1061
• Mutation(s): No 


• Deposited: 2024-03-11 Released: 2025-03-26 
• Deposition Author(s): Williamson, A., Walker, E., Kelton, W., Hicks, J.
• Funding Organization(s): Health Research Council (HRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of a nanobody against a conserved lipooligosaccharide motif of N. gonorrhoeae

Walker, E., Warrender, A., Beijerling, K., Kelson, J., Pan, J., Williamson, A., Hicks, J., Kelton, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 39.31 kDa 
• Atom Count: 2,168 
• Modeled Residue Count: 276 
• Deposited Residue Count: 370 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GA10 nanobody	A, B	167	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclized peptide	C, D	18	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.229 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.878	α = 88.86
b = 31.631	β = 87.08
c = 69.783	γ = 89.24

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Williamson, A., Walker, E., Kelton, W., Hicks, J.

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	21/794

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release