4WLF | pdb_00004wlf

Crystal structure of L-malate bound MDH2

• PDB DOI: https://doi.org/10.2210/pdb4WLF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-07 Released: 2015-11-25 
• Deposition Author(s): Eo, Y.M., Han, B.G., Ahn, H.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of L-malate bound MDH2

Eo, Y.M., Han, B.G., Ahn, H.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 144.34 kDa 
• Atom Count: 9,351 
• Modeled Residue Count: 1,256 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malate dehydrogenase, mitochondrial	A, B, C, D	340	Homo sapiens	Mutation(s): 0  Gene Names: MDH2 EC: 1.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P40926 (Homo sapiens) Explore P40926  Go to UniProtKB:  P40926
PHAROS:  P40926 GTEx:  ENSG00000146701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMR	E [auth A], G [auth B], I [auth C], K [auth D]	(2S)-2-hydroxybutanedioic acid C4 H6 O5 BJEPYKJPYRNKOW-REOHCLBHSA-N
PO4	F [auth A], H [auth B], J [auth C], L [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.246	α = 90
b = 152.183	β = 90
c = 155.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Eo, Y.M., Han, B.G., Ahn, H.C.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description