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)

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
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Ligand Structure Quality Assessment

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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

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4JZK0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.