Research workbench
Crystal structure of aldehyde dehydrogenase from burkholderia thailandensis in covelent complex with NADPH
Analyse Crystal structure of aldehyde dehydrogenase from burkholderia thailandensis in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J6B
- Type
- protein
- Length
- 1,910 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- Q2T801
- Ligands
- NDP, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase | protein | 481 | 42% helix, 22% strand | Q2T801 |
| B, C | Aldehyde dehydrogenase | protein | 476 | 42% helix, 22% strand | Q2T801 |
| D | Aldehyde dehydrogenase | protein | 477 | 43% helix, 22% strand | Q2T801 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 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 | 711 | 0.86 | 0.90 | 75 | empty |
| 2 | 327 | 0.81 | 0.91 | 37 | empty |
| 3 | 294 | 0.81 | 0.92 | 32 | empty |
| 4 | 415 | 0.77 | 0.86 | 35 | empty |
| 5 | 393 | 0.76 | 0.86 | 38 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3058 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 3028 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 991 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 989 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 Q2T801
- Elsewhere: RCSB PDB 5J6B · PDBe 5J6B · UniProt Q2T801
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.