Research workbench
Thermostable aldehyde dehydrogenase from pyrobaculum sp. complexed with NADP+ at 2 a resolution
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
- 4NMJ
- Type
- protein
- Length
- 3,880 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.-
- UniProt
- G7VCG0
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 486 | 42% helix, 23% strand | G7VCG0 |
| B, E | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 485 | 43% helix, 22% strand | G7VCG0 |
| C, H | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 484 | 43% helix, 23% strand | G7VCG0 |
| D | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 483 | 42% helix, 22% strand | G7VCG0 |
| F | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 489 | 42% helix, 22% strand | G7VCG0 |
| G | Aldehyde dehydrogenase (EC 1.2.1.-) | protein | 484 | 43% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.91 | 0.93 | 133 | empty |
| 2 | 1088 | 0.91 | 0.93 | 121 | empty |
| 3 | 645 | 0.87 | 0.91 | 82 | empty |
| 4 | 618 | 0.87 | 0.91 | 78 | empty |
| 5 | 599 | 0.86 | 0.91 | 74 | empty |
Interfaces
13 interfaces between chains.
- C–D · 3693 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3677 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3668 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 3619 Ų buried · 55 hydrogen bonds · protein-protein
- E–H · 1232 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4NMJ · Thermostable aldehyde dehydrogenase from Pyrobaculum sp. complexed with NADP+ at 2 A… · 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 4NMJ · PDBe 4NMJ · UniProt G7VCG0
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