5MH5

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-2-hydroxyacid dehydrogenase
A, B
308Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4)Mutation(s): 0 
Gene Names: ddh (serA5)
EC: 1.1.1.-
Find proteins for Q2VEQ7 (Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4))
Go to UniProtKB:  Q2VEQ7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7N5
Query on 7N5

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

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.530α = 90.00
b = 87.400β = 96.34
c = 66.100γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Cootmodel building
Aimlessdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: 2018-05-02
    Type: Initial release