Research workbench
Human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid
Analyse Human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FHZ
- Type
- protein
- Length
- 3,818 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens
- Molecule
- Aldehyde dehydrogenase family 1 member A3
- EC
- 1.2.1.5
- UniProt
- P47895
- Ligands
- NAD, REA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · resolution 2.9 · 8 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 489 | 39% helix, 23% strand | P47895 |
| B | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 475 | 38% helix, 24% strand | P47895 |
| C | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 489 | 39% helix, 22% strand | P47895 |
| D | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 488 | 40% helix, 24% strand | P47895 |
| E | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 478 | 40% helix, 21% strand | P47895 |
| F | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 449 | 40% helix, 22% strand | P47895 |
| G | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 462 | 40% helix, 24% strand | P47895 |
| H | Aldehyde dehydrogenase family 1 member A3 (EC 1.2.1.5) | protein | 488 | 40% helix, 23% strand | P47895 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- REA · Retinoic acid · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.90 | 0.93 | 118 | empty |
| 2 | 870 | 0.90 | 0.92 | 98 | empty |
| 3 | 743 | 0.82 | 0.85 | 72 | empty |
| 4 | 688 | 0.81 | 0.85 | 72 | empty |
| 5 | 750 | 0.81 | 0.85 | 72 | empty |
Interfaces
14 interfaces between chains.
- E–F · 2710 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 2696 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2682 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2615 Ų buried · 50 hydrogen bonds · protein-protein
- F–H · 1112 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5FHZ · Human aldehyde dehydrogenase 1A3 complexed with NAD(+) and retinoic acid · the same entry in another collection · chain H against H, TM-score 1.00
- P47895 · AlphaFold monomer V2.0 prediction for aldehyde dehydrogenase family 1 member A3 (P47895) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P47895
- Elsewhere: RCSB PDB 5FHZ · PDBe 5FHZ · UniProt P47895
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