9Y4U | pdb_00009y4u

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)

• PDB DOI: https://doi.org/10.2210/pdb9Y4U/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neisseria gonorrhoeae NCCP11945
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-03 Released: 2025-09-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)

Lovell, S., Cooper, A., Battaile, K.P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.99 kDa 
• Atom Count: 5,087 
• Modeled Residue Count: 629 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase	A, B	342	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0  Gene Names: NGK_2321 EC: 1.2.1
UniProt
Find proteins for B4RPP8 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RPP8  Go to UniProtKB:  B4RPP8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M39Y4U

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.189	α = 90
b = 123.985	β = 90
c = 130.745	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release