MolNFT v1 · #125223 · protein

Crystal structure of ALDH1A1 in complex with BUC22

5L2O · Retinal dehydrogenase 1: “Crystal structure of ALDH1A1 in complex with BUC22”. X-ray diffraction, 3 ligands (6ZW, YB, CL), 20 pockets (best druggability 0.87). MolNFT v1 #125223 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5L2O
Type: protein
Length: 3,947 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Retinal dehydrogenase 1
EC: 1.2.1.-, 1.2.1.36
UniProt: P00352
Ligands: 6ZW, YB, CL
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G	Retinal dehydrogenase 1 (EC 1.2.1.-, 1.2.1.36)	protein	494	41% helix, 22% strand	P00352
C, D, E, F, H	Retinal dehydrogenase 1 (EC 1.2.1.-, 1.2.1.36)	protein	493	41% helix, 22% strand	P00352

Ligands and binding sites

6ZW · 7-(diethylamino)-4-methyl-2H-1-benzopyran-2-one · ligand · 8 copies · chains A, B, C, D, E, F, G, H
YB · Ytterbium (III) ion · metal · 8 copies · chains A, B, D, E, F, G, H
CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H

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	450	0.87	0.94	72	CL
2	1055	0.87	0.88	140	6ZW
3	338	0.87	0.96	31	empty
4	1060	0.86	0.87	142	6ZW
5	319	0.86	0.96	30	empty

Interfaces

12 interfaces between chains.

C–D · 2956 Å² buried · 55 hydrogen bonds · protein-protein
G–H · 2952 Å² buried · 55 hydrogen bonds · protein-protein
A–B · 2948 Å² buried · 56 hydrogen bonds · protein-protein
E–F · 2933 Å² buried · 55 hydrogen bonds · protein-protein
B–C · 1547 Å² buried · 31 hydrogen bonds · protein-protein

Compared structures

5L2O · Crystal Structure of ALDH1A1 in complex with BUC22 · the same entry in another collection · chain E against E, TM-score 1.00
P00352 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 1 (P00352) · a predicted model of the same protein · chain D 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 P00352
Elsewhere: RCSB PDB 5L2O · PDBe 5L2O · UniProt P00352

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