9Z9C | pdb_00009z9c

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

PDB DOI: https://doi.org/10.2210/pdb9Z9C/pdb

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

Deposited: 2025-11-18 Released: 2025-11-26
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.232 (Depositor), 0.233 (DCC)
R-Value Work:
0.194 (Depositor), 0.199 (DCC)
R-Value Observed:
0.196 (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 form)

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

To be published.

Macromolecule Content

Total Structure Weight: 899.99 kDa
Atom Count: 60,606
Modeled Residue Count: 7,897
Deposited Residue Count: 8,208
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, U, V, W, X	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 AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth J] SDF format, chain JA [auth K] SDF format, chain KA [auth L] SDF format, chain LA [auth M] SDF format, chain MA [auth N] SDF format, chain NA [auth O] SDF format, chain OA [auth P] SDF format, chain PA [auth Q] SDF format, chain QA [auth R] SDF format, chain RA [auth S] SDF format, chain SA [auth T] SDF format, chain TA [auth U] SDF format, chain UA [auth V] SDF format, chain VA [auth W] SDF format, chain WA [auth X] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth M] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth O] MOL2 format, chain OA [auth P] MOL2 format, chain PA [auth Q] MOL2 format, chain QA [auth R] MOL2 format, chain RA [auth S] MOL2 format, chain SA [auth T] MOL2 format, chain TA [auth U] MOL2 format, chain UA [auth V] MOL2 format, chain VA [auth W] MOL2 format, chain WA [auth X] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth M] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth O] mmCIF format, chain OA [auth P] mmCIF format, chain PA [auth Q] mmCIF format, chain QA [auth R] mmCIF format, chain RA [auth S] mmCIF format, chain SA [auth T] mmCIF format, chain TA [auth U] mmCIF format, chain UA [auth V] mmCIF format, chain VA [auth W] mmCIF format, chain WA [auth X] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth B]	AA [auth C] BA [auth D] CA [auth E] DA [auth F] EA [auth G] AA [auth C], BA [auth D], CA [auth E], DA [auth F], EA [auth G], FA [auth H], HA [auth I], IA [auth J], JA [auth K], KA [auth L], LA [auth M], MA [auth N], NA [auth O], OA [auth P], PA [auth Q], QA [auth R], RA [auth S], SA [auth T], TA [auth U], UA [auth V], VA [auth W], WA [auth X], Y [auth A], Z [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth M] Focus chain MA [auth N] Focus chain NA [auth O] Focus chain OA [auth P] Focus chain PA [auth Q] Focus chain QA [auth R] Focus chain RA [auth S] Focus chain SA [auth T] Focus chain TA [auth U] Focus chain UA [auth V] Focus chain VA [auth W] Focus chain WA [auth X] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth E] Focus chain DA [auth F] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth K] Focus chain KA [auth L] Focus chain LA [auth M] Focus chain MA [auth N] Focus chain NA [auth O] Focus chain OA [auth P] Focus chain PA [auth Q] Focus chain QA [auth R] Focus chain RA [auth S] Focus chain SA [auth T] Focus chain TA [auth U] Focus chain UA [auth V] Focus chain VA [auth W] Focus chain WA [auth X] Focus chain Y [auth A] Focus chain Z [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain GA [auth H] MOL2 format, chain GA [auth H] mmCIF format, chain GA [auth H]	GA [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain GA [auth H] Interactions & Density Focus chain GA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.232 (Depositor), 0.233 (DCC)
R-Value Work: 0.194 (Depositor), 0.199 (DCC)
R-Value Observed: 0.196 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39Z9C

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.534	α = 85.95
b = 137.842	β = 77.63
c = 157.786	γ = 86.88

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: 2025-11-26

Deposition Author(s):

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