5MH6

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.128 

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 dehydrogenaseABCD308Haloferax 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
NAD
Query on NAD

Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
7N5
Query on 7N5

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

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

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A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.128 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.455α = 109.11
b = 75.008β = 107.55
c = 77.555γ = 95.91
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release