6ITK

Crystal strcuture of malate dehydrogenase from Corynebacterium glutamicum ATCC 13032 in complex with NAD and malate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Unraveling the truth about malate dehydrogenase of Mannheimia succiniciproducens that has been constraining mass production of succinic acid

Ahn, J.H.Seo, H.Park, W.Seok, J.Lee, J.A.Kim, W.J.Kim, K.-J.Lee, S.Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A, B
336Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)Mutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for Q8NN33 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  Q8NN33
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

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

Download SDF File 
Download CCD File 
A, B
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.931α = 90.00
b = 116.940β = 95.31
c = 66.003γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-11-23 
  • Released Date: 2019-11-27 
  • Deposition Author(s): Seo, H., Kim, K.-J.

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release