MolNFT v1 · #117838 · protein
Thermostable aldehyde dehydrogenase from pyrobaculum sp. 1860 complexed with NADP and isobutyraldehyde
5EK6: “Thermostable aldehyde dehydrogenase from pyrobaculum sp. 1860 complexed with NADP and isobutyraldehyde”. X-ray diffraction, 2 ligands (NAP, 5OZ), 20 pockets (best druggability 0.90). MolNFT v1 #117838 on GenesisL1: 3D structure…
- PDB
- 5EK6
- Type
- protein
- Length
- 3,869 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- G7VCG0
- Ligands
- NAP, 5OZ
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Aldehyde dehydrogenase | protein | 482 | 42% helix, 23% strand | G7VCG0 |
| B, E, G | Aldehyde dehydrogenase | protein | 484 | 42% helix, 23% strand | G7VCG0 |
| C, D | Aldehyde dehydrogenase | protein | 485 | 43% helix, 22% strand | G7VCG0 |
| H | Aldehyde dehydrogenase | protein | 483 | 42% helix, 23% strand | G7VCG0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 5OZ · 2-methylpropanal · ligand · 6 copies · chains A, B, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.90 | 0.92 | 139 | empty |
| 2 | 1049 | 0.90 | 0.92 | 132 | empty |
| 3 | 629 | 0.87 | 0.92 | 73 | empty |
| 4 | 640 | 0.86 | 0.90 | 80 | empty |
| 5 | 548 | 0.86 | 0.91 | 74 | empty |
Interfaces
13 interfaces between chains.
- E–F · 3626 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3610 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3593 Ų buried · 57 hydrogen bonds · protein-protein
- G–H · 3572 Ų buried · 52 hydrogen bonds · protein-protein
- E–H · 1233 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5EK6 · Thermostable aldehyde dehydrogenase from Pyrobaculum sp. 1860 complexed with NADP and… · the same entry in another collection · 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 G7VCG0
- Elsewhere: RCSB PDB 5EK6 · PDBe 5EK6 · UniProt G7VCG0
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