MolNFT v1 · #98018 · protein

Crystal structure analysis of ALDH2+ALDIB13

4KWG · Aldehyde dehydrogenase, mitochondrial: “Crystal structure analysis of ALDH2+ALDIB13”. X-ray diffraction, 3 ligands (GAI, 2AK, NA), 20 pockets (best druggability 0.90). MolNFT v1 #98018 on GenesisL1: 3D structure, binding sites and…

PDB: 4KWG
Type: protein
Length: 3,952 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, 2AK, NA
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3)	protein	494	40% helix, 21% strand	P05091

Ligands and binding sites

GAI · Guanidine · ligand · 7 copies · chains A, B, C, D, E, F, G, H
2AK · 7-bromo-5-methyl-1H-indole-2,3-dione · ligand · 2 copies · chains A, H
NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
EDO · 1,2-ethanediol · additive · 8 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	866	0.90	0.93	71	empty
2	432	0.86	0.94	44	empty
3	423	0.86	0.93	40	empty
4	442	0.85	0.93	46	empty
5	434	0.85	0.93	40	empty

Interfaces

14 interfaces between chains.

C–D · 2895 Å² buried · 53 hydrogen bonds · protein-protein
A–B · 2892 Å² buried · 46 hydrogen bonds · protein-protein
E–F · 2873 Å² buried · 50 hydrogen bonds · protein-protein
G–H · 2834 Å² buried · 49 hydrogen bonds · protein-protein
E–H · 1625 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

4KWG · Crystal Structure Analysis of ALDH2+ALDiB13 · 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 E 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 4KWG · PDBe 4KWG · UniProt P05091

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