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The crystal structure of the pseudomonas dacunhae aspartate-beta- decarboxylase reveals a novel oligomeric assembly for a pyridoxal-5- phosphate dependent enzyme
Analyse The crystal structure of the pseudomonas dacunhae aspartate-beta- decarboxylase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FDD
- Type
- protein
- Length
- 502 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-aspartate-beta-decarboxylase
- EC
- 4.1.1.12
- UniProt
- Q845W8
- Ligands
- PLP, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-aspartate-beta-decarboxylase (EC 4.1.1.12) | protein | 502 | 52% helix, 12% strand | Q845W8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.61 | 0.82 | 37 | empty |
| 2 | 68 | 0.59 | 0.90 | 20 | PLP |
| 3 | 117 | 0.45 | 0.77 | 21 | empty |
| 4 | 88 | 0.37 | 0.76 | 17 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3FDD · The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a… · 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 Q845W8
- Elsewhere: RCSB PDB 3FDD · PDBe 3FDD · UniProt Q845W8
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