Research workbench
Crystal structure of human aldehyde dehydrogenase-2 in complex with nitroglycerin
Analyse Crystal structure of human aldehyde dehydrogenase-2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FR8
- Type
- protein
- Length
- 3,948 residues
- Chains
- 8
- 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, NAD, ADP, TNG, MG, NA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, H | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 493 | 40% helix, 22% strand | P05091 |
| C | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 496 | 40% helix, 21% strand | P05091 |
| G | Aldehyde dehydrogenase, mitochondrial (EC 1.2.1.3) | protein | 494 | 40% helix, 21% strand | P05091 |
Ligands and binding sites
- URE · Urea · ligand · 6 copies · chains A, B, C, D, E, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, C, D, F
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains B, E, G, H
- TNG · propane-1,2,3-triyl trinitrate · ligand · chains A
- MG · Magnesium ion · metal · 8 copies · chains C, E, F, H
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.90 | 0.93 | 71 | empty |
| 2 | 453 | 0.86 | 0.93 | 42 | empty |
| 3 | 395 | 0.85 | 0.93 | 52 | empty |
| 4 | 433 | 0.85 | 0.92 | 51 | empty |
| 5 | 359 | 0.84 | 0.93 | 37 | empty |
Interfaces
14 interfaces between chains.
- A–B · 2888 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2880 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2856 Ų buried · 51 hydrogen bonds · protein-protein
- G–H · 2840 Ų buried · 48 hydrogen bonds · protein-protein
- E–H · 1641 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 4FR8 · Crystal structure of human aldehyde dehydrogenase-2 in complex with nitroglycerin · 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 B 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 4FR8 · PDBe 4FR8 · UniProt P05091
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