9UGT | pdb_00009ugt

Structure of Butanol Dehydrogenase in Complex with ADP and Co

• PDB DOI: https://doi.org/10.2210/pdb9UGT/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Fusobacterium nucleatum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-04-13 Released: 2025-10-29 
• Deposition Author(s): Bai, X., Meng, D., Nam, K.H., Xu, Y.B.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Flexibility of the Nicotinamide Group of the NADP Cofactor in Butanol Dehydrogenase YqdH from Fusobacterium nucleatum

Bai, X., Xu, Y.B., Nam, K.H.

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

Macromolecule Content 

• Total Structure Weight: 43.82 kDa 
• Atom Count: 3,062 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent butanol dehydrogenase A	A	385	Fusobacterium nucleatum	Mutation(s): 0  Gene Names: FN1415 EC: 1.1.1
UniProt
Find proteins for Q8R612 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8R612  Go to UniProtKB:  Q8R612

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CO (Subject of Investigation/LOI)	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.426	α = 90
b = 79.351	β = 90
c = 212.932	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Bai, X., Meng, D., Nam, K.H., Xu, Y.B.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF- 2017M3A9F6029736
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020M3H1A1075314
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838

Revision History  

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