1V59 | pdb_00001v59

Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb1V59/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2003-11-21 Released: 2005-02-15 
• Deposition Author(s): Adachi, W., Suzuki, K., Tsunoda, M., Sekiguchi, T., Reed, L.J., Takenaka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.203 (Depositor) 

Literature

Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+

Adachi, W., Suzuki, K., Tsunoda, M., Sekiguchi, T., Reed, L.J., Takenaka, A.

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: 106.24 kDa 
• Atom Count: 7,799 
• Modeled Residue Count: 956 
• Deposited Residue Count: 956 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoamide dehydrogenase	A, B	478	Saccharomyces cerevisiae	Mutation(s): 0  EC: 1.8.1.4
UniProt
Find proteins for P09624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09624  Go to UniProtKB:  P09624

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAD	E [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.6	α = 90
b = 96.4	β = 90
c = 160.1	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Adachi, W., Suzuki, K., Tsunoda, M., Sekiguchi, T., Reed, L.J., Takenaka, A.

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-12-25
  Changes: Derived calculations, Structure summary