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Crystal structure analysis of ALDH1B1

Analyse Crystal structure analysis of ALDH1B1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RAD
Type: protein
Length: 986 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase X, mitochondrial
EC: 1.2.1.3
UniProt: P30837
Ligands: NAD, ZGJ, NA
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aldehyde dehydrogenase X, mitochondrial (EC 1.2.1.3)	protein	493	40% helix, 22% strand	P30837

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
ZGJ · 3-(2-methoxyphenyl)-1-(4-phenylphenyl)-6,7,8,9-tetrahydro-5~{H}-imidazo[1,2-a][1,3]diazepine · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 8 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	422	0.86	0.94	34	empty
2	376	0.67	0.81	49	NAD
3	353	0.66	0.80	44	NAD
4	259	0.65	0.82	31	ZGJ
5	229	0.62	0.82	37	ZGJ

Interfaces

1 interface between chains.

A–B · 2844 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

7RAD · Crystal Structure Analysis of ALDH1B1 · the same entry in another collection · chain A against A, TM-score 1.00
P30837 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase X, mitochondrial (P30837) · a predicted model of the same protein · chain A 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 P30837
Elsewhere: RCSB PDB 7RAD · PDBe 7RAD · UniProt P30837

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