Research workbench
Crystal structure of Tyrosine decarboxylase in complex with PLP
Analyse Crystal structure of Tyrosine decarboxylase in complex with PLP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LIV
- Type
- protein
- Length
- 2,892 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.31
- Source
- Papaver somniferum
- Molecule
- Tyrosine/DOPA decarboxylase 2
- EC
- 4.1.1.28, 4.1.1.25
- UniProt
- P54769
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.31 · 4 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Tyrosine/DOPA decarboxylase 2 (EC 4.1.1.28, 4.1.1.25) | protein | 485 | 52% helix, 12% strand | P54769 |
| B, D | Tyrosine/DOPA decarboxylase 2 (EC 4.1.1.28, 4.1.1.25) | protein | 483 | 52% helix, 12% strand | P54769 |
| E | Tyrosine/DOPA decarboxylase 2 (EC 4.1.1.28, 4.1.1.25) | protein | 479 | 48% helix, 13% strand | P54769 |
| F | Tyrosine/DOPA decarboxylase 2 (EC 4.1.1.28, 4.1.1.25) | protein | 477 | 48% helix, 13% strand | P54769 |
Ligands and binding sites
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.80 | 0.81 | 111 | empty |
| 2 | 1000 | 0.80 | 0.81 | 90 | GOL |
| 3 | 697 | 0.77 | 0.82 | 67 | GOL |
| 4 | 1000 | 0.76 | 0.79 | 96 | GOL |
| 5 | 72 | 0.74 | 0.98 | 26 | empty |
Interfaces
9 interfaces between chains.
- C–D · 6720 Ų buried · 114 hydrogen bonds · protein-protein
- A–B · 6675 Ų buried · 111 hydrogen bonds · protein-protein
- E–F · 6533 Ų buried · 81 hydrogen bonds · protein-protein
- B–D · 671 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 624 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (cofactor).
Compared structures
- 6LIV · Crystal structure of tyrosine decarboxylase in complex with plp · the same entry in another collection · chain F against F, TM-score 1.00
- P54769 · AlphaFold monomer V2.0 prediction for TYROSINE/DOPA decarboxylase 2 (P54769) · a predicted model of the same protein · chain B 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 P54769
- Elsewhere: RCSB PDB 6LIV · PDBe 6LIV · UniProt P54769
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