MolNFT v1 · #54951 · protein
Crystal structure of E257Q mutant of the box pathway encoded aldh from burkholderia xenovorans LB400
2Y53 · Aldehyde dehydrogenase (box pathway): “Crystal structure of E257Q mutant of the box pathway encoded aldh from burkholderia xenovorans LB400”. X-ray diffraction, 1 ligand (NAP), 14 pockets (best druggability 0.82). MolNFT v1 #54951…
- 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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