9ZAO | pdb_00009zao

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)

PDB DOI: https://doi.org/10.2210/pdb9ZAO/pdb

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

Deposited: 2025-11-19 Released: 2025-12-24
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.234 (Depositor), 0.231 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

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

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)

Liu, L., Lovell, S., Seibold, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 745.31 kDa
Atom Count: 49,857
Modeled Residue Count: 6,646
Deposited Residue Count: 6,840
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	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4RPP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain DA [auth I] SDF format, chain EA [auth J] SDF format, chain FA [auth K] SDF format, chain GA [auth L] SDF format, chain HA [auth N] SDF format, chain JA [auth Q] SDF format, chain KA [auth T] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth E] SDF format, chain AA [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth J] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth N] MOL2 format, chain JA [auth Q] MOL2 format, chain KA [auth T] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain AA [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain EA [auth J] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain HA [auth N] mmCIF format, chain JA [auth Q] mmCIF format, chain KA [auth T] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain AA [auth F]	AA [auth F] CA [auth H] DA [auth I] EA [auth J] FA [auth K] AA [auth F], CA [auth H], DA [auth I], EA [auth J], FA [auth K], GA [auth L], HA [auth N], JA [auth Q], KA [auth T], U [auth A], W [auth B], Y [auth D], Z [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth N] Focus chain JA [auth Q] Focus chain KA [auth T] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth J] Focus chain FA [auth K] Focus chain GA [auth L] Focus chain HA [auth N] Focus chain JA [auth Q] Focus chain KA [auth T] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth D] Focus chain Z [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain IA [auth O] SDF format, chain V [auth A] SDF format, chain X [auth C] MOL2 format, chain BA [auth G] MOL2 format, chain IA [auth O] MOL2 format, chain V [auth A] MOL2 format, chain X [auth C] mmCIF format, chain BA [auth G] mmCIF format, chain IA [auth O] mmCIF format, chain V [auth A] mmCIF format, chain X [auth C]	BA [auth G], IA [auth O], V [auth A], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain IA [auth O] Focus chain V [auth A] Focus chain X [auth C] Interactions & Density Focus chain BA [auth G] Focus chain IA [auth O] Focus chain V [auth A] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.234 (Depositor), 0.231 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.358	α = 76.3
b = 139.715	β = 87.32
c = 222.702	γ = 88.12

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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