2EQ6

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2EQ6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-30 Released: 2008-04-01 
• Deposition Author(s): Nakai, T., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.219 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Starting Model: experimental

Literature

Crystal structure of lipoamide dehydrogenase from Thermus thermophilus HB8

Nakai, T., Kamiya, N.

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)

Macromolecule Content

• Total Structure Weight: 99.87 kDa 
• Atom Count: 7,581 
• Modelled Residue Count: 920 
• Deposited Residue Count: 928 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component	A, B	464	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0233 EC: 1.8.1.4
UniProt
Find proteins for Q5SLR0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLR0  Go to UniProtKB:  Q5SLR0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.219 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.323	α = 93.26
b = 62.683	β = 107.39
c = 73.562	γ = 108.71

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Nakai, T., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary