9FOB | pdb_00009fob

Glyceraldehyde 3-phosphate Dehydrogenase (GapA) from Helicobacter pylori in Complex with NAPD (Holo)

• PDB DOI: https://doi.org/10.2210/pdb9FOB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori 26695
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-11 Released: 2025-06-25 
• Deposition Author(s): Elliott, P.R., Moody, P.C.E.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.241 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Structure and coenzyme specificity of a Helicobacter pylori glyceraldehyde 3-phosphate dehydrogenase (GapA)

Foster, S., Eliott, P.R., Basran, J., Moody, P.C.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 153.42 kDa 
• Atom Count: 10,792 
• Modeled Residue Count: 1,347 
• Deposited Residue Count: 1,372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase (Gap)	A, B, C, D	343	Helicobacter pylori 26695	Mutation(s): 0  Gene Names: HP_1346
UniProt
Find proteins for O25902 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O25902  Go to UniProtKB:  O25902

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], H [auth B], I [auth C], J [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MOH	F [auth A], G [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.241 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.938	α = 90
b = 116.938	β = 90
c = 95.474	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Elliott, P.R., Moody, P.C.E.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release