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Crystal structure of apo MDH2

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

PDB: 4WLN
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: PO4
Pockets: 12 · best druggability 0.75

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

PO4 · Phosphate ion · ion · 12 copies · chains A, B, C, D

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

Pockets

12 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	348	0.75	0.86	47	PO4
2	296	0.73	0.86	47	PO4
3	270	0.71	0.85	45	PO4
4	291	0.69	0.84	41	PO4
5	257	0.49	0.74	38	empty

Interfaces

4 interfaces between chains.

C–D · 1601 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 1590 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 462 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 456 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4WLN · Crystal structure of apo 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 4WLN · PDBe 4WLN · UniProt P40926

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