Macromolecule Content

Total Structure Weight: 146.84 kDa
Atom Count: 9514
Residue Count: 1256
Unique protein chains: 1

4WLV

Crystal structure of NAD bound MDH2

DOI: 10.2210/pdb4WLV/pdb

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

Deposited: 2014-10-08 Released: 2015-11-25
Deposition Author(s): Eo, Y.M., Han, B.G., Ahn, H.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of NAD bound MDH2

Eo, Y.M., Han, B.G., Ahn, H.C.

To be published.

Macromolecules

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(by identity cutoff) | Structure

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
Find proteins for P40926 (Homo sapiens) Explore P40926 Go to UniProtKB: P40926
NIH Common Fund Data Resources
PHAROS: P40926 GTEx: ENSG00000146701
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain H [B] SDF format, chain K [C] SDF format, chain N [D] MOL2 format, chain E [A] MOL2 format, chain H [B] MOL2 format, chain K [C] MOL2 format, chain N [D]	A, B, C, D	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain I [B] SDF format, chain J [B] SDF format, chain L [C] SDF format, chain M [C] SDF format, chain O [D] SDF format, chain P [D] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain I [B] MOL2 format, chain J [B] MOL2 format, chain L [C] MOL2 format, chain M [C] MOL2 format, chain O [D] MOL2 format, chain P [D]	A, B, C, D	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.248
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.864	α = 90
b = 152.016	β = 90
c = 155.669	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-10-08
Released Date: 2015-11-25

Deposition Author(s):

Revision History

Version 1.0: 2015-11-25
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.