9ZAG | pdb_00009zag

Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb9ZAG/pdb

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

Deposited: 2025-11-19 Released: 2025-12-03
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: 1.91 Å
R-Value Free:
0.187 (Depositor), 0.194 (DCC)
R-Value Work:
0.155 (Depositor), 0.163 (DCC)
R-Value Observed:
0.156 (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 and GLYCERALDEHYDE-3-PHOSPHATE

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

To be published.

Macromolecule Content

Total Structure Weight: 303.19 kDa
Atom Count: 21,909
Modeled Residue Count: 2,667
Deposited Residue Count: 2,736
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	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 8 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 D] SDF format, chain GA [auth E] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain OA [auth G] SDF format, chain P [auth B] SDF format, chain SA [auth H] SDF format, chain W [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain W [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain OA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain W [auth C]	CA [auth D] GA [auth E] KA [auth F] L [auth A] OA [auth G] CA [auth D], GA [auth E], KA [auth F], L [auth A], OA [auth G], P [auth B], SA [auth H], W [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain P [auth B] Focus chain SA [auth H] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth E] Focus chain KA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain P [auth B] Focus chain SA [auth H] Focus chain W [auth C]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain RA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain RA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain RA [auth H]	BA [auth D], RA [auth H]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain RA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain RA [auth H]
G3H (Subject of Investigation/LOI) Query on G3H Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain MA [auth G] SDF format, chain N [auth B] SDF format, chain QA [auth H] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	EA [auth E] I [auth A] IA [auth F] MA [auth G] N [auth B] EA [auth E], I [auth A], IA [auth F], MA [auth G], N [auth B], QA [auth H], T [auth C], Y [auth D]	GLYCERALDEHYDE-3-PHOSPHATE C₃ H₇ O₆ P LXJXRIRHZLFYRP-VKHMYHEASA-N		Interactions Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain N [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain N [auth B] Focus chain QA [auth H] Focus chain T [auth C] Focus chain Y [auth D]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth F] SDF format, chain K [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain Z [auth D]	FA [auth E] J [auth A] JA [auth F] K [auth A] NA [auth G] FA [auth E], J [auth A], JA [auth F], K [auth A], NA [auth G], O [auth B], U [auth C], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain NA [auth G] Focus chain O [auth B] Focus chain U [auth C] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain V [auth C]	AA [auth D], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain HA [auth E] SDF format, chain LA [auth F] SDF format, chain M [auth A] SDF format, chain PA [auth G] SDF format, chain Q [auth B] SDF format, chain TA [auth H] SDF format, chain X [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain X [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain X [auth C]	DA [auth D] HA [auth E] LA [auth F] M [auth A] PA [auth G] DA [auth D], HA [auth E], LA [auth F], M [auth A], PA [auth G], Q [auth B], TA [auth H], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain TA [auth H] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain TA [auth H] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.187 (Depositor), 0.194 (DCC)
R-Value Work: 0.155 (Depositor), 0.163 (DCC)
R-Value Observed: 0.156 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39ZAG

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.647	α = 90
b = 105.543	β = 94.63
c = 167.699	γ = 90

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: 2025-12-03

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