MolNFT v1 · #91878 · protein
Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2
4FQF · Aldehyde dehydrogenase, mitochondrial: “Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2”. X-ray diffraction, 5 ligands (URE, 2NO, NAD), 16 pockets (best druggability 0.90). MolNFT v1 #91878 on…
- PDB
- 4FQF
- Type
- protein
- Length
- 1,967 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase, mitochondrial
- EC
- 1.2.1.3
- UniProt
- P05091
- Ligands
- URE, 2NO, NAD, MG, NA
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 488 | 41% helix, 22% strand | P05091 |
| B, C, D | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 493 | 40% helix, 23% strand | P05091 |
Ligands and binding sites
- URE · Urea · ligand · 6 copies · chains A, B, C, D
- 2NO · Nitrogen dioxide · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.90 | 0.93 | 70 | empty |
| 2 | 431 | 0.85 | 0.93 | 41 | empty |
| 3 | 989 | 0.84 | 0.85 | 154 | 2NO, NAD |
| 4 | 165 | 0.82 | 0.98 | 35 | URE |
| 5 | 179 | 0.82 | 0.97 | 39 | URE |
Interfaces
6 interfaces between chains.
- C–D · 2913 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2877 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 1613 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1606 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1173 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4FQF · Crystal structure of a thionitrate intermediate of human aldehyde dehydrogenase-2 · the same entry in another collection · chain D against D, TM-score 1.00
- P05091 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase, mitochondrial (P05091) · a predicted model of the same protein · chain C 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 4FQF · PDBe 4FQF · UniProt P05091
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