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Crystal structure of L-malate and NAD bound MDH2

Analyse Crystal structure of L-malate and NAD bound MDH2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4WLU
Type: protein
Length: 1,256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase, mitochondrial
EC: 1.1.1.37
UniProt: P40926
Ligands: LMR, NAD
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Malate dehydrogenase, mitochondrial (EC 1.1.1.37)	protein	314	49% helix, 19% strand	P40926

Ligands and binding sites

LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B, C, D
NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.74	0.87	48	LMR, NAD
2	297	0.72	0.86	48	LMR, NAD
3	267	0.72	0.86	40	LMR, NAD
4	314	0.71	0.84	49	LMR, NAD
5	91	0.46	0.80	15	empty

Interfaces

4 interfaces between chains.

C–D · 1595 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 1584 Å² buried · 33 hydrogen bonds · protein-protein
B–D · 464 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 444 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4WLU · Crystal structure of L-malate and NAD bound MDH2 · the same entry in another collection · chain A against A, TM-score 1.00
P40926 · AlphaFold monomer V2.0 prediction for malate dehydrogenase, mitochondrial (P40926) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P40926
Elsewhere: RCSB PDB 4WLU · PDBe 4WLU · UniProt P40926

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