5MHA

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with a mixture of 2-ketohexanoic acid and 2-hydroxyhexanoic acid, and NADPH (1.57 A resolution)

• PDB DOI: https://doi.org/10.2210/pdb5MHA/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Haloferax mediterranei ATCC 33500
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-11-23 Released: 2018-05-09 
• Deposition Author(s): Bisson, C., Baker, P.J., Domenech Perez, J., Pramanpol, N., Harding, S.E., Rice, D.W., Ferrer, J.
• Funding Organization(s): University of Alicante, Biotechnology and Biological Sciences Research Council, Wellcome Trust, Wolfson Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Productive ternary complexes of D-2-hydroxyacid dehydrogenase provide insights into the chiral specificity of its reaction mechanism

Domenech Perez, J., Pramanpol, N., Baker, P.J., Bisson, C., Harding, S.E., Rice, D.W., Ferrer, J.

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: 69.38 kDa 
• Atom Count: 5,342 
• Modelled Residue Count: 616 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-2-hydroxyacid dehydrogenase	A, B	308	Haloferax mediterranei ATCC 33500	Mutation(s): 0  Gene Names: ddh, serA5, HFX_2024 EC: 1.1.1
UniProt
Find proteins for Q2VEQ7 (Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4)) Explore Q2VEQ7  Go to UniProtKB:  Q2VEQ7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	M [auth A], W [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
7N6	V [auth B]	(2R)-2-hydroxyhexanoic acid C6 H12 O3 NYHNVHGFPZAZGA-RXMQYKEDSA-N
7N5	L [auth A], U [auth B]	2-Ketohexanoic acid C6 H10 O3 XNIHZNNZJHYHLC-UHFFFAOYSA-N
SO4	N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], O [auth B], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.54	α = 90
b = 76.3	β = 97.04
c = 66.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Bisson, C., Baker, P.J., Domenech Perez, J., Pramanpol, N., Harding, S.E., Rice, D.W., Ferrer, J.

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Funding Organization	Location	Grant Number
University of Alicante	Spain	VIGROB046
Biotechnology and Biological Sciences Research Council	United Kingdom	--
Wellcome Trust	United Kingdom	--
Wolfson Foundation	United Kingdom	--

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 2.0: 2022-12-28
  Changes: Atomic model, Database references, Derived calculations
• Version 3.0: 2024-06-19
  Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy