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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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.