9GV3 | pdb_00009gv3

Crystal structure of the complex between Nb474 mutant R53A,D125A and Trypanosoma congolense fructose-1,6-bisphosphate aldolase

• PDB DOI: https://doi.org/10.2210/pdb9GV3/pdb

• Classification: LYASE
• Organism(s): Trypanosoma congolense IL3000, Vicugna pacos
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-21 Released: 2025-10-01 
• Deposition Author(s): McNae, I.W., Dornan, J., Walkinshaw, M.D.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

The role of water in tuning nanobody-antigen recognition

Hacisuleyman, A., Dorna, J., McNae, I., Wear, M., Bilal, T., Yuan, M., Michels, P.A.M., Pinto Torres, J.E., Magez, S., Sterckx, Y.G.J., Erman, E., Walkinshaw, M.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 233.84 kDa 
• Atom Count: 16,673 
• Modeled Residue Count: 1,987 
• Deposited Residue Count: 2,120 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase	A, B, C, D	387	Trypanosoma congolense IL3000	Mutation(s): 0  Gene Names: TCIL3000_10_4760 EC: 4.1.2.13
UniProt
Find proteins for G0UWE7 (Trypanosoma congolense (strain IL3000)) Explore G0UWE7  Go to UniProtKB:  G0UWE7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb474 mutant R53A,D125A	E, F, G, H	143	Vicugna pacos	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	I [auth B], J [auth B], K [auth C], L [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.495	α = 90
b = 111.166	β = 90
c = 123.244	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): McNae, I.W., Dornan, J., Walkinshaw, M.D.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	092076
Wellcome Trust	United Kingdom	203149

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release