9KQ1 | pdb_00009kq1

Crystal structure of L-2-keto-3-deoxypentonate 4-dehydrogenase bound to NAD(H)

• PDB DOI: https://doi.org/10.2210/pdb9KQ1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Herbaspirillum huttiense
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2024-11-25 Released: 2025-11-26 
• Deposition Author(s): Akagashi, M., Watanabe, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.269 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: in silico

Literature

2-keto-3-deoxypentonate 4-dehydrogenase

Akagashi, M., Watanabe, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 54.96 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 491 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SDR superfamily	A, B	248	Herbaspirillum huttiense	Mutation(s): 0
UniProt
Find proteins for A0ABU2ELG5 (Herbaspirillum huttiense subsp. lycopersici) Explore A0ABU2ELG5  Go to UniProtKB:  A0ABU2ELG5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.269 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.879	α = 90
b = 85.293	β = 90
c = 134.823	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Akagashi, M., Watanabe, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release