MolNFT v1 · #47072 · protein

ARG475GLN mutant of human mitochondrial aldehyde dehydrogenase, complexed with NAD+

2ONP: “ARG475GLN mutant of human mitochondrial aldehyde dehydrogenase, complexed with NAD+”. X-ray diffraction, 4 ligands (GAI, NAD, MG), 20 pockets (best druggability 0.89). MolNFT v1 #47072 on GenesisL1: 3D structure, binding sites and…

PDB: 2ONP
Type: protein
Length: 3,952 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aldehyde dehydrogenase
EC: 1.2.1.3
UniProt: P05091
Ligands: GAI, NAD, MG, NA
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Aldehyde dehydrogenase (EC 1.2.1.3)	protein	494	41% helix, 22% strand	P05091

Ligands and binding sites

GAI · Guanidine · ligand · 28 copies · chains A, B, C, D, E, F, G, H
NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, F, G, H
NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
EDO · 1,2-ethanediol · additive · 39 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	797	0.89	0.93	80	empty
2	795	0.89	0.93	73	empty
3	191	0.83	0.97	40	EDO
4	213	0.83	0.96	40	EDO
5	193	0.83	0.97	36	EDO

Interfaces

13 interfaces between chains.

G–H · 2809 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2797 Å² buried · 32 hydrogen bonds · protein-protein
E–F · 2794 Å² buried · 33 hydrogen bonds · protein-protein
A–B · 2780 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 1609 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

2ONP · Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, complexed with NAD+ · 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 G 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 2ONP · PDBe 2ONP · UniProt P05091

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