MolNFT v1 · #54961 · protein
Crystal structure of C296A mutant of the box pathway encoded aldh from burkholderia xenovorans LB400
2Y5D · Aldehyde dehydrogenase (box pathway): “Crystal structure of C296A mutant of the box pathway encoded aldh from burkholderia xenovorans LB400”. X-ray diffraction, 1 ligand (NAP), 11 pockets (best druggability 0.82). MolNFT v1 #54961…
- PDB
- 2Y5D
- Type
- protein
- Length
- 1,048 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
- 11 · 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 | 521 | 40% helix, 22% strand | Q13WK4 |
| B | Aldehyde dehydrogenase (box pathway) | protein | 527 | 40% helix, 22% strand | Q13WK4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- P6G · Hexaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.82 | 0.83 | 73 | GOL |
| 2 | 515 | 0.67 | 0.78 | 76 | P6G, NAP |
| 3 | 370 | 0.65 | 0.79 | 56 | P6G, NAP |
| 4 | 177 | 0.46 | 0.75 | 29 | empty |
| 5 | 130 | 0.44 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2885 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2Y5D · Crystal structure of C296A 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 2Y5D · PDBe 2Y5D · UniProt Q13WK4
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