8E2N | pdb_00008e2n

Crystal Structure of Nanobody VHH113 Specific for PA14 Cif

• PDB DOI: https://doi.org/10.2210/pdb8E2N/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vicugna pacos
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-08-15 Released: 2023-10-04 
• Deposition Author(s): Simard, A.R., Madden, D.R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cystic Fibrosis Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Convergent strategies for nanobody-mediated inhibition of an epoxide hydrolase

Simard, A.R., Taher, N.M., Beauchemin, K.S., Mishra, A.K., Hederman, A.P., Hampton, T.H., Vasylieva, N., Morisseau, C., Ackerman, M.E., Madden, D.R.

(2026) J Struct Biol X : 100166

• DOI: https://doi.org/10.1016/j.yjsbx.2026.100166

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 28.14 kDa 
• Atom Count: 2,360 
• Modeled Residue Count: 265 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH113	A [auth B], B [auth A]	134	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.083	α = 90
b = 51.607	β = 90
c = 75.991	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Simard, A.R., Madden, D.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI091699
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK117469
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI007519
Cystic Fibrosis Foundation	United States	STANTO19R0

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description
• Version 1.3: 2026-10-21
  Changes: Database references