Research workbench
Crystal structure of E257Q mutant of the box pathway encoded aldh from burkholderia xenovorans LB400
Analyse Crystal structure of E257Q mutant of the box pathway encoded aldh from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y53
- Type
- protein
- Length
- 1,053 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldehyde dehydrogenase (box pathway)
- UniProt
- Q13WK4
- Ligands
- NAP
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldehyde dehydrogenase (box pathway) | protein | 529 | 39% helix, 22% strand | Q13WK4 |
| B | Aldehyde dehydrogenase (box pathway) | protein | 524 | 40% helix, 22% strand | Q13WK4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, 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 | 1190 | 0.82 | 0.83 | 90 | GOL |
| 2 | 127 | 0.58 | 0.84 | 28 | GOL |
| 3 | 119 | 0.57 | 0.84 | 27 | GOL |
| 4 | 354 | 0.55 | 0.74 | 47 | NAP |
| 5 | 337 | 0.55 | 0.74 | 43 | NAP |
Interfaces
1 interface between chains.
- A–B · 2952 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2Y53 · Crystal structure of E257Q mutant of the box pathway encoded ALDH from Burkholderia… · 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 2Y53 · PDBe 2Y53 · UniProt Q13WK4
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