9YWI | pdb_00009ywi

Crystal structure of a Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (monoclinic P form)

PDB DOI: https://doi.org/10.2210/pdb9YWI/pdb

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

Deposited: 2025-10-24 Released: 2025-11-05
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: 2.00 Å
R-Value Free:
0.203 (Depositor), 0.205 (DCC)
R-Value Work:
0.169 (Depositor), 0.175 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (monoclinic P form)

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

To be published.

Macromolecule Content

Total Structure Weight: 302.58 kDa
Atom Count: 22,450
Modeled Residue Count: 2,697
Deposited Residue Count: 2,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain NA [auth G] SDF format, chain K [auth A] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain K [auth A] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain K [auth A]	K [auth A], NA [auth G], U [auth B], W [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain NA [auth G] Focus chain U [auth B] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain NA [auth G] Focus chain U [auth B] Focus chain W [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain QA [auth H] SDF format, chain SA [auth H] SDF format, chain Z [auth C] SDF format, chain X [auth B] SDF format, chain T [auth B] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain GA [auth E] SDF format, chain BA [auth D] MOL2 format, chain QA [auth H] MOL2 format, chain SA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth B] MOL2 format, chain T [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain QA [auth H] mmCIF format, chain SA [auth H] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth B] mmCIF format, chain T [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] GA [auth E] J [auth A] JA [auth F] QA [auth H] BA [auth D], GA [auth E], J [auth A], JA [auth F], QA [auth H], SA [auth H], T [auth B], X [auth B], Z [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain QA [auth H] Focus chain SA [auth H] Focus chain T [auth B] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain QA [auth H] Focus chain SA [auth H] Focus chain T [auth B] Focus chain X [auth B] Focus chain Z [auth C]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain FA [auth E] MOL2 format, chain FA [auth E] mmCIF format, chain FA [auth E]	FA [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain FA [auth E] Interactions & Density Focus chain FA [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain V [auth B] SDF format, chain S [auth B] SDF format, chain RA [auth H] SDF format, chain OA [auth G] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth G] SDF format, chain L [auth A] SDF format, chain KA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain S [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain S [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth F]	EA [auth E] KA [auth F] L [auth A] MA [auth G] N [auth A] EA [auth E], KA [auth F], L [auth A], MA [auth G], N [auth A], O [auth A], OA [auth G], RA [auth H], S [auth B], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain KA [auth F] Focus chain L [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth G] Focus chain RA [auth H] Focus chain S [auth B] Focus chain V [auth B] Interactions & Density Focus chain EA [auth E] Focus chain KA [auth F] Focus chain L [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth G] Focus chain RA [auth H] Focus chain S [auth B] Focus chain V [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain PA [auth H] SDF format, chain P [auth B] SDF format, chain LA [auth G] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain LA [auth G] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth E] DA [auth E] HA [auth F] I [auth A] AA [auth D], CA [auth E], DA [auth E], HA [auth F], I [auth A], IA [auth F], LA [auth G], P [auth B], PA [auth H], Q [auth B], R [auth B], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain LA [auth G] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203 (Depositor), 0.205 (DCC)
R-Value Work: 0.169 (Depositor), 0.175 (DCC)
R-Value Observed: 0.171 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39YWI

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.467	α = 90
b = 122.984	β = 90.11
c = 150.567	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

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