9PG6 | pdb_00009pg6

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)

PDB DOI: https://doi.org/10.2210/pdb9PG6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Bordetella pertussis Tohama I
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-07-07 Released: 2025-07-16
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: 2.15 Å
R-Value Free:
0.230 (Depositor), 0.233 (DCC)
R-Value Work:
0.193 (Depositor), 0.199 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: in silico
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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 Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (NAD bound)

Liu, L., Ung, A.R., Lovell, S., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 304.31 kDa
Atom Count: 21,477
Modeled Residue Count: 2,689
Deposited Residue Count: 2,752
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	344	Bordetella pertussis Tohama I	Mutation(s): 0 Gene Names: gap, hexC, BP1000 EC: 1.2.1
UniProt
Find proteins for Q7VZB9 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)) Explore Q7VZB9 Go to UniProtKB: Q7VZB9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7VZB9
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 I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain S [auth G] SDF format, chain T [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H]	I [auth A] K [auth B] M [auth C] N [auth D] P [auth E] I [auth A], K [auth B], M [auth C], N [auth D], P [auth E], Q [auth F], S [auth G], T [auth H]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain S [auth G] Focus chain T [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain O [auth D] SDF format, chain R [auth F] SDF format, chain U [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] MOL2 format, chain R [auth F] MOL2 format, chain U [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth D] mmCIF format, chain R [auth F] mmCIF format, chain U [auth H]	J [auth A], L [auth B], O [auth D], R [auth F], U [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D] Focus chain R [auth F] Focus chain U [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth D] Focus chain R [auth F] Focus chain U [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.230 (Depositor), 0.233 (DCC)
R-Value Work: 0.193 (Depositor), 0.199 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39PG6

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.826	α = 90
b = 130.061	β = 90.86
c = 140.967	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: 2025-07-16

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