9FQ4 | pdb_00009fq4

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NADP holoenzyme, from Helicobacter pylori, with active site cysteine oxidised to sulfenic acid

PDB DOI: https://doi.org/10.2210/pdb9FQ4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-14 Released: 2025-06-25
Deposition Author(s): Foster, S.P., Moody, P.C.E.
Funding Organization(s): Royal Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.137 (Depositor), 0.136 (DCC)
R-Value Work:
0.120 (Depositor), 0.119 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) apoenzyme, from Helicobacter pylori

Foster, S.P., Moody, P.C.E.

To be published.

Macromolecule Content

Total Structure Weight: 36.94 kDa
Atom Count: 2,948
Modeled Residue Count: 330
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase (Gap)	A	330	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O25902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD Query on CSD	A	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.137 (Depositor), 0.136 (DCC)
R-Value Work: 0.120 (Depositor), 0.119 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.478	α = 90
b = 96.196	β = 90
c = 94.728	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
xia2.multiplex	data scaling
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Royal Society	United Kingdom	--

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.