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


Ligand Structure Quality Assessment 


This is version 2.0 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D-2-hydroxyacid dehydrogenase
A, B, C, D
308Haloferax mediterranei ATCC 33500Mutation(s): 0 
Gene Names: ddhserA5HFX_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VEQ7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
HA [auth B],
KB [auth D],
S [auth A],
XA [auth C]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
7N5
Query on 7N5

Download Ideal Coordinates CCD File 
IA [auth B],
LB [auth D],
T [auth A],
YA [auth C]
2-Ketohexanoic acid
C6 H10 O3
XNIHZNNZJHYHLC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth B],
EB [auth D],
K [auth A],
QA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BB [auth D]
CB [auth D]
DB [auth D]
AA [auth B],
AB [auth D],
BB [auth D],
CB [auth D],
DB [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth C],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
FB [auth D]
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
FB [auth D],
GA [auth B],
GB [auth D],
HB [auth D],
IB [auth D],
JB [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
RA [auth C],
SA [auth C],
TA [auth C],
U [auth A],
UA [auth C],
VA [auth C],
WA [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
JA [auth C],
ZA [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


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  (Full details and data files)

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