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

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
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Ligand Structure Quality Assessment

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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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06959
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9P0
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 D [auth B] SDF format, chain E [auth C] MOL2 format, chain D [auth B] MOL2 format, chain E [auth C] mmCIF format, chain D [auth B] mmCIF format, chain E [auth C]	D [auth B], E [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth B] Focus chain E [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth C]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Zajec Hudnik, T.

Glockshuber, R.

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

Revision History (Full details and data files)

Version 1.0: 2025-10-29
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.