9H2I | pdb_00009h2i

Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate dehydrogenase complex

• PDB DOI: https://doi.org/10.2210/pdb9H2I/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2025-10-29 
• Deposition Author(s): Bothe, S.N., Zajec Hudnik, T., Glockshuber, R.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

A cooperative binding mechanism steers the recruitment of peripheral subunits in the E. coli pyruvate dehydrogenase complex

Bothe, S.N., Racunica, D., Zajec Hudnik, T., Zdanowicz, R., Bothe, A., Giese, C., Glockshuber, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local 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: 110.03 kDa 
• Atom Count: 8,146 
• Modeled Residue Count: 990 
• Deposited Residue Count: 1,012 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	A	66	Escherichia coli	Mutation(s): 0  Gene Names: aceF, b0115, JW0111 EC: 2.3.1.12
UniProt
Find proteins for P06959 (Escherichia coli (strain K12)) Explore P06959  Go to UniProtKB:  P06959

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	B, C	473	Escherichia coli	Mutation(s): 0  Gene Names: lpdA, lpd, b0116, JW0112 EC: 1.8.1.4
UniProt
Find proteins for P0A9P0 (Escherichia coli (strain K12)) Explore P0A9P0  Go to UniProtKB:  P0A9P0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.703	α = 90
b = 88.353	β = 90
c = 200.687	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Bothe, S.N., Zajec Hudnik, T., Glockshuber, R.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

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