2EJV | pdb_00002ejv

Crystal structure of threonine 3-dehydrogenase complexed with NAD+

• PDB DOI: https://doi.org/10.2210/pdb2EJV/pdb

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


• Deposited: 2007-03-20 Released: 2008-03-25 
• Deposition Author(s): Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of threonine 3-dehydrogenase

Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.95 kDa 
• Atom Count: 5,401 
• Modeled Residue Count: 686 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-threonine 3-dehydrogenase	A, B	343	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.1.1.103
UniProt
Find proteins for Q5SKS4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKS4  Go to UniProtKB:  Q5SKS4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.236 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.758	α = 90
b = 135.758	β = 90
c = 268.593	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Omi, R., Yao, T., Goto, M., Miyahara, I., Hirotsu, K.

Revision History  

• Version 1.0: 2008-03-25
  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