Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148967.03 
• Atom Count: 9501 
• Residue Count: 1368 
• Unique protein chains: 1

2DFD

Crystal Structure of Human Malate Dehydrogenase Type 2

• DOI: 10.2210/pdb2DFD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2006-02-28 Released: 2006-03-28 
• Deposition Author(s): Ugochukwu, E., Shafqat, N., Rojkova, A., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.194 
• R-Value Work: 0.156 

Literature

Crystal Structure of Human Malate Dehydrogenase Type 2

Ugochukwu, E., Shafqat, N., Rojkova, A., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Malate dehydrogenase	A, B, C, D	342	Homo sapiens	Mutation(s): 0  Gene Names: MDH2 EC: 1.1.1.37
Find proteins for P40926 (Homo sapiens) Go to Gene View: MDH2 Go to UniProtKB:  P40926

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MLT	A, B, C, D	D-MALATE (2R)-2-HYDROXYBUTANEDIOIC ACID; 2-HYDROXY-SUCCINIC ACID C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
CL	A, B, C, D	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NAD	A, B, C, D	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ALA	A	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
HIS	A, B, C	HISTIDINE C6 H10 N3 O2 HNDVDQJCIGZPNO-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.194 
• R-Value Work: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.943	α = 90.00
b = 152.526	β = 90.00
c = 154.827	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
CCP4	data scaling
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-28 
• Released Date: 2006-03-28 
• Deposition Author(s): Ugochukwu, E., Shafqat, N., Rojkova, A., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., von Delft, F., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2006-03-28
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance