Research workbench
Crystal structure of C296A mutant of the box pathway encoded aldh from burkholderia xenovorans LB400
Analyse Crystal structure of C296A 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
- 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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