9KD2 | pdb_00009kd2

Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan

• PDB DOI: https://doi.org/10.2210/pdb9KD2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides ovatus ATCC 8483
• Expression System: Escherichia coli B
• Mutation(s): No 


• Deposited: 2024-11-02 Released: 2025-10-29 
• Deposition Author(s): Takase, R., Mikami, B., Hashimoto, W.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Yakult Bio-science Foundation, Japan Foundation for Applied Enzymology, Japan Environ and Organic-farming Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan

Takase, R., Mikami, B., Hashimoto, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 181.44 kDa 
• Atom Count: 11,858 
• Modeled Residue Count: 1,551 
• Deposited Residue Count: 1,650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, short chain dehydrogenase/reductase family protein	A, B, C, D, E, F	275	Bacteroides ovatus ATCC 8483	Mutation(s): 0  Gene Names: BACOVA_00141
UniProt
Find proteins for A0AAN3ACT3 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153)) Explore A0AAN3ACT3  Go to UniProtKB:  A0AAN3ACT3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.943	α = 90
b = 126.911	β = 102.38
c = 71.657	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Takase, R., Mikami, B., Hashimoto, W.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	15H04629
Japan Society for the Promotion of Science (JSPS)	Japan	18H02166
Japan Society for the Promotion of Science (JSPS)	Japan	21H02156
Yakult Bio-science Foundation	Japan	--
Japan Foundation for Applied Enzymology	Japan	--
Japan Environ and Organic-farming Foundation	Japan	--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release