Research workbench
Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa
Analyse Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JS3
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dopa decarboxylase
- EC
- 4.1.1.28
- UniProt
- P80041
- Ligands
- PLP, 142, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dopa decarboxylase (EC 4.1.1.28) | protein | 464 | 51% helix, 14% strand | P80041 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 142 · Carbidopa · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.78 | 0.98 | 28 | empty |
| 2 | 360 | 0.70 | 0.83 | 41 | PLP, 142 |
| 3 | 346 | 0.69 | 0.82 | 38 | PLP, 142 |
| 4 | 113 | 0.42 | 0.76 | 21 | empty |
| 5 | 101 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 5782 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 1JS3 · Crystal structure of dopa decarboxylase in complex with the inhibitor carbidopa · the same entry in another collection · chain A against A, TM-score 1.00
- P80041 · AlphaFold monomer V2.0 prediction for aromatic-L-amino-acid decarboxylase (P80041) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P80041
- Elsewhere: RCSB PDB 1JS3 · PDBe 1JS3 · UniProt P80041
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