3W8F

Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor malonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

X-ray diffraction of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and malonate

Kanazawa, H.Tsunoda, M.Hoque, M.M.Suzuki, K.Yamamoto, T.Takenaka, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-3-hydroxybutyrate dehydrogenase
A
260Alcaligenes faecalisMutation(s): 0 
EC: 1.1.1.30
Find proteins for D0VWQ0 (Alcaligenes faecalis)
Go to UniProtKB:  D0VWQ0
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
A
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.142 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.830α = 90.00
b = 62.830β = 90.00
c = 119.290γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
ADSCdata collection
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Non-polymer description