MolNFT v1 · #2479 · protein

Sheep liver class 1 aldehyde dehydrogenase with NAD bound

1BXS: “Sheep liver class 1 aldehyde dehydrogenase with NAD bound”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.87). MolNFT v1 #2479 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1BXS
Type: protein
Length: 1,976 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase
EC: 1.2.1.3
UniProt: P51977
Ligands: NAD
Pockets: 20 · best druggability 0.87

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Aldehyde dehydrogenase (EC 1.2.1.3)	protein	494	40% helix, 21% strand	P51977

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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	595	0.87	0.92	45	empty
2	312	0.84	0.95	31	empty
3	308	0.84	0.95	32	empty
4	612	0.81	0.86	95	NAD
5	132	0.80	0.98	31	empty

Interfaces

6 interfaces between chains.

A–B · 3050 Å² buried · 45 hydrogen bonds · protein-protein
C–D · 3035 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 1526 Å² buried · 32 hydrogen bonds · protein-protein
A–D · 1524 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 974 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1BXS · Sheep liver class 1 aldehyde dehydrogenase with NAD bound · the same entry in another collection · chain C against C, TM-score 1.00
P51977 · AlphaFold monomer V2.0 prediction for retinal dehydrogenase 1 (P51977) · 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 P51977
Elsewhere: RCSB PDB 1BXS · PDBe 1BXS · UniProt P51977

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