MolNFT v1 · #108892 · protein

Crystal structure of L-malate bound MDH2

4WLF · Malate dehydrogenase, mitochondrial: “Crystal structure of L-malate bound MDH2”. X-ray diffraction, 2 ligands (LMR, PO4), 10 pockets (best druggability 0.75). MolNFT v1 #108892 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4WLF
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, PO4
Pockets: 10 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 47% 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	47% helix, 19% strand	P40926

Ligands and binding sites

LMR · (2S)-2-hydroxybutanedioic acid · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D

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

Pockets

10 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	343	0.75	0.86	50	LMR, PO4
2	253	0.71	0.86	48	LMR, PO4
3	270	0.70	0.85	46	LMR, PO4
4	301	0.68	0.83	43	LMR, PO4
5	83	0.45	0.81	17	empty

Interfaces

4 interfaces between chains.

A–B · 1599 Å² buried · 31 hydrogen bonds · protein-protein
C–D · 1597 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 473 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 461 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4WLF · Crystal structure of L-malate 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 0.99

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 4WLF · PDBe 4WLF · UniProt P40926

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