Research workbench
Structure of tyrosine decarboxylase complex with plp at 1.9 ångströms resolution
Analyse Structure of tyrosine decarboxylase complex with plp at 1.9 ångströms resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HSJ
- Type
- protein
- Length
- 1,201 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative decarboxylase
- EC
- 4.1.1.25
- UniProt
- J7GQ11
- Ligands
- PLP
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative decarboxylase (EC 4.1.1.25) | protein | 606 | 50% helix, 14% strand | J7GQ11 |
| B | Putative decarboxylase (EC 4.1.1.25) | protein | 595 | 52% helix, 14% strand | J7GQ11 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.83 | 0.84 | 122 | PLP |
| 2 | 84 | 0.75 | 0.98 | 28 | empty |
| 3 | 568 | 0.73 | 0.81 | 63 | PLP |
| 4 | 245 | 0.70 | 0.85 | 44 | empty |
| 5 | 153 | 0.53 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 6875 Ų buried · 88 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5HSJ · Structure of tyrosine decarboxylase complex with PLP at 1.9 Angstroms resolution · the same entry in another collection · chain A against A, TM-score 1.00
- J7GQ11 · AlphaFold monomer V2.0 prediction for L-tyrosine decarboxylase (J7GQ11) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 J7GQ11
- Elsewhere: RCSB PDB 5HSJ · PDBe 5HSJ · UniProt J7GQ11
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