MolNFT v1 · #34075 · protein

Structure of the malate dehydrogenase from aeropyrum pernix

2D4A: “Structure of the malate dehydrogenase from aeropyrum pernix”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #34075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2D4A
Type: protein
Length: 1,206 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Malate dehydrogenase
EC: 1.1.1.37
UniProt: Q9YEA1
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Malate dehydrogenase (EC 1.1.1.37)	protein	301	50% helix, 23% strand	Q9YEA1
A	Malate dehydrogenase (EC 1.1.1.37)	protein	298	50% helix, 20% strand	Q9YEA1
D	Malate dehydrogenase (EC 1.1.1.37)	protein	308	51% helix, 20% strand	Q9YEA1
C	Malate dehydrogenase (EC 1.1.1.37)	protein	299	50% helix, 20% strand	Q9YEA1

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.85	0.89	58	empty
2	614	0.85	0.90	61	empty
3	531	0.74	0.82	49	empty
4	205	0.72	0.88	28	empty
5	358	0.67	0.81	48	empty

Interfaces

6 interfaces between chains.

D–C · 2116 Å² buried · 25 hydrogen bonds · protein-protein
B–A · 2093 Å² buried · 30 hydrogen bonds · protein-protein
A–D · 979 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 964 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 362 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2D4A · Structure of the malate dehydrogenase from Aeropyrum pernix · the same entry in another collection · chain C against C, TM-score 1.00
Q9YEA1 · AlphaFold monomer V2.0 prediction for malate dehydrogenase (Q9YEA1) · 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 Q9YEA1
Elsewhere: RCSB PDB 2D4A · PDBe 2D4A · UniProt Q9YEA1

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