MolNFT v1 · #72421 · protein

Human mitochondrial aldehyde dehydrogenase, apo form

3N80 · Aldehyde dehydrogenase, mitochondrial: “Human mitochondrial aldehyde dehydrogenase, apo form”. X-ray diffraction, 3 ligands (GAI, NA, MG), 20 pockets (best druggability 0.86). MolNFT v1 #72421 on GenesisL1: 3D structure, binding…

PDB: 3N80
Type: protein
Length: 3,953 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase, mitochondrial
EC: 1.2.1.3
UniProt: P05091
Ligands: GAI, NA, MG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3)	protein	494	41% helix, 22% strand	P05091
E	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3)	protein	495	40% helix, 22% strand	P05091

Ligands and binding sites

GAI · Guanidine · ligand · 21 copies · chains A, B, C, D, E, F, G, H
NA · Sodium ion · metal · 7 copies · chains B, C, D, E, F, G, H
MG · Magnesium ion · metal · chains H
EDO · 1,2-ethanediol · additive · 36 copies · chains A, B, D, C, E, F, H, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	404	0.86	0.94	40	EDO
2	390	0.86	0.94	36	empty
3	383	0.86	0.94	41	empty
4	398	0.85	0.93	40	EDO
5	396	0.85	0.94	41	empty

Interfaces

13 interfaces between chains.

G–H · 2861 Å² buried · 55 hydrogen bonds · protein-protein
E–F · 2846 Å² buried · 52 hydrogen bonds · protein-protein
A–B · 2827 Å² buried · 51 hydrogen bonds · protein-protein
C–D · 2815 Å² buried · 47 hydrogen bonds · protein-protein
E–H · 1607 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (oxidation).

Compared structures

3N80 · Human mitochondrial aldehyde dehydrogenase, apo form · the same entry in another collection · chain H against H, TM-score 1.00
P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain F against A, TM-score 1.00

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 P05091
Elsewhere: RCSB PDB 3N80 · PDBe 3N80 · UniProt P05091

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