9W61 | pdb_00009w61

Butyryl CoA dehydrogenase with FAD

• PDB DOI: https://doi.org/10.2210/pdb9W61/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Faecalibacterium prausnitzii L2-6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-08-03 Released: 2025-11-26 
• Deposition Author(s): Park, S.H., Bang, K.H., Seo, M.J., Hwang, K.Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structural insights into butyryl-CoA dehydrogenase and its modeled complex with electron transferring flavoprotein from Faecalibacterium prausnitzii L2-6

Park, S., Bang, K., Shin, B., Park, I., Hawkes, H.J.K., Kim, S., Hwang, K.Y.

(2025) Appl Biol Chem 68: 79

• DOI: https://doi.org/10.1186/s13765-025-01052-3

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 173.22 kDa 
• Atom Count: 12,094 
• Modeled Residue Count: 1,522 
• Deposited Residue Count: 1,556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyryl CoA Dehydrogenase with FAD	A, B, C, D	389	Faecalibacterium prausnitzii L2-6	Mutation(s): 0  EC: 1.3.99.2
UniProt
Find proteins for D4JZK0 (Faecalibacterium prausnitzii L2-6) Explore D4JZK0  Go to UniProtKB:  D4JZK0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.566	α = 90
b = 106.299	β = 117.76
c = 91.954	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Park, S.H., Bang, K.H., Seo, M.J., Hwang, K.Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

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