MolNFT v1 · #108907 · protein

Crystal structure of NAD bound MDH2

4WLV · Malate dehydrogenase, mitochondrial: “Crystal structure of NAD bound MDH2”. X-ray diffraction, 2 ligands (NAD, PO4), 6 pockets (best druggability 0.78). MolNFT v1 #108907 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WLV
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: NAD, PO4
Pockets: 6 · best druggability 0.78

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

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 8 copies · chains A, B, C, D

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1185	0.78	0.80	133	NAD, PO4
2	764	0.74	0.79	82	NAD, PO4
3	413	0.70	0.81	55	NAD, PO4
4	212	0.46	0.73	30	empty
5	205	0.42	0.72	33	empty

Interfaces

4 interfaces between chains.

C–D · 1614 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1581 Å² buried · 32 hydrogen bonds · protein-protein
B–D · 436 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 433 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

4WLV · Crystal structure of 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 0.99

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 4WLV · PDBe 4WLV · UniProt P40926

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