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)


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 

wwPDB Validation   3D Report Full Report



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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-2-hydroxyacid dehydrogenaseAB308Haloferax mediterranei ATCC 33500Mutation(s): 0 
Gene Names: ddhserA5HFX_2024
EC: 1.1.1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
7N6
Query on 7N6

Download CCD File 
B
(2R)-2-hydroxyhexanoic acid
C6 H12 O3
NYHNVHGFPZAZGA-RXMQYKEDSA-N
 Ligand Interaction
7N5
Query on 7N5

Download CCD File 
A, B
2-Ketohexanoic acid
C6 H10 O3
XNIHZNNZJHYHLC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 62.54α = 90
b = 76.3β = 97.04
c = 66.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of AlicanteSpainVIGROB046
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--
Wellcome TrustUnited Kingdom--
Wolfson FoundationUnited Kingdom--

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release