Research workbench
Crystal structure of an aldedhyde dehydrogenase from burkholderia vietnamiensis
Analyse Crystal structure of an aldedhyde dehydrogenase from burkholderia vietnamiensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KF0
- Type
- protein
- Length
- 1,908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- UniProt
- A4JLJ7
- Ligands
- NDP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase | protein | 480 | 41% helix, 22% strand | A4JLJ7 |
| B, C, D | Aldehyde dehydrogenase | protein | 476 | 42% helix, 22% strand | A4JLJ7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 13 copies · chains A, B, D, C
- ACT · Acetate ion · additive · 7 copies · chains A, B, C, D
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 5 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 | 450 | 0.82 | 0.90 | 47 | MPD |
| 2 | 412 | 0.81 | 0.89 | 51 | empty |
| 3 | 342 | 0.80 | 0.90 | 47 | empty |
| 4 | 358 | 0.77 | 0.88 | 37 | MPD |
| 5 | 368 | 0.77 | 0.88 | 38 | MPD |
Interfaces
6 interfaces between chains.
- A–B · 3218 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 3198 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 1087 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1087 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 745 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5KF0 · Crystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis · 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 A4JLJ7
- Elsewhere: RCSB PDB 5KF0 · PDBe 5KF0 · UniProt A4JLJ7
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