9W16 | pdb_00009w16

3-hydroxybutyryl-CoA dehydrogenase with NAD

PDB DOI: https://doi.org/10.2210/pdb9W16/pdb

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

Deposited: 2025-07-25 Released: 2026-04-15
Deposition Author(s): Shin, B.M.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural Basis for Substrate-Induced Activation of 3-Hydroxybutyryl-CoA Dehydrogenase from Faecalibacterium prausnitzii L2-6

Shin, B.M., Park, S.H., Park, I.G., Bang, K.H., Kim, S.H., Hwang, K.Y.

To be published.

Macromolecule Content

Total Structure Weight: 187.32 kDa
Atom Count: 13,048
Modeled Residue Count: 1,740
Deposited Residue Count: 1,740
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxyacyl-CoA dehydrogenase, NAD binding domain protein	A [auth D] B [auth F] C [auth E] D [auth C] E [auth B] A [auth D], B [auth F], C [auth E], D [auth C], E [auth B], F [auth A]	290	Faecalibacterium prausnitzii L2-6	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E] mmCIF format, chain G [auth E]	G [auth E]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.963	α = 90
b = 147.782	β = 90
c = 167.444	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-15

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: 2026-04-15
Type: Initial release

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.