Research workbench
Crystal structure of aldehyde dehydrogenase from burkholderia xenovorans LB400
Analyse Crystal structure of aldehyde dehydrogenase from burkholderia xenovorans LB400 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VRO
- Type
- protein
- Length
- 1,048 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase
- EC
- 1.2.1.3
- UniProt
- Q13WK4
- Ligands
- NDP, ETE
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 521 | 39% helix, 22% strand | Q13WK4 |
| B | Aldehyde dehydrogenase (EC 1.2.1.3) | protein | 527 | 39% helix, 22% strand | Q13WK4 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- ETE · 2-{2-[2-2-(methoxy-ethoxy)-ethoxy]-ethoxy}-ethanol · ligand · chains A
- P6G · Hexaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.84 | 0.85 | 87 | empty |
| 2 | 117 | 0.60 | 0.85 | 27 | ETE |
| 3 | 115 | 0.58 | 0.85 | 28 | P6G |
| 4 | 312 | 0.56 | 0.76 | 46 | NDP |
| 5 | 229 | 0.52 | 0.76 | 32 | NDP |
Interfaces
1 interface between chains.
- A–B · 2939 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 2VRO · Crystal structure of aldehyde dehydrogenase from Burkholderia xenovorans LB400 · 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 Q13WK4
- Elsewhere: RCSB PDB 2VRO · PDBe 2VRO · UniProt Q13WK4
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