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Crystal structure of human aldehyde dehydrogenase, ALDH1A2

Analyse Crystal structure of human aldehyde dehydrogenase, ALDH1A2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X2Q
Type: protein
Length: 1,892 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinal dehydrogenase 2
EC: 1.2.1.36
UniProt: O94788
Ligands: NAD
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Retinal dehydrogenase 2 (EC 1.2.1.36)	protein	472	38% helix, 21% strand	O94788
C, D	Retinal dehydrogenase 2 (EC 1.2.1.36)	protein	474	39% helix, 21% strand	O94788

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	501	0.85	0.91	48	empty
2	142	0.79	0.97	31	empty
3	110	0.79	0.97	19	empty
4	427	0.78	0.87	61	empty
5	104	0.78	0.97	19	empty

Interfaces

6 interfaces between chains.

C–D · 2282 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 2197 Å² buried · 20 hydrogen bonds · protein-protein
A–D · 1712 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1704 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 946 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4X2Q · Crystal Structure of Human Aldehyde Dehydrogenase, ALDH1a2 · the same entry in another collection · chain D against D, TM-score 1.00
O94788 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 2 (O94788) · a predicted model of the same protein · chain B 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 O94788
Elsewhere: RCSB PDB 4X2Q · PDBe 4X2Q · UniProt O94788

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