Research workbench
Thermostable aldehyde dehydrogenase from pyrobaculum sp. complexed with NADP+
Analyse Thermostable aldehyde dehydrogenase from pyrobaculum sp. complexed with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H73
- Type
- protein
- Length
- 3,872 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- G7VCG0
- Ligands
- NDP, NI
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase | protein | 482 | 42% helix, 23% strand | G7VCG0 |
| B, C, D, F | Aldehyde dehydrogenase | protein | 485 | 41% helix, 23% strand | G7VCG0 |
| E, H | Aldehyde dehydrogenase | protein | 483 | 41% helix, 24% strand | G7VCG0 |
| G | Aldehyde dehydrogenase | protein | 484 | 42% helix, 23% strand | G7VCG0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D, E, F, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.91 | 0.93 | 95 | NI |
| 2 | 781 | 0.89 | 0.93 | 86 | NI |
| 3 | 584 | 0.87 | 0.92 | 76 | empty |
| 4 | 570 | 0.86 | 0.92 | 73 | empty |
| 5 | 577 | 0.86 | 0.91 | 77 | empty |
Interfaces
13 interfaces between chains.
- E–F · 3776 Ų buried · 63 hydrogen bonds · protein-protein
- G–H · 3765 Ų buried · 61 hydrogen bonds · protein-protein
- A–B · 3744 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3721 Ų buried · 59 hydrogen bonds · protein-protein
- F–G · 1240 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4H73 · Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ · 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 4H73 · PDBe 4H73 · UniProt G7VCG0
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