Research workbench
K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii complexed with a post-decarboxylation quinonoid-like intermediate formed with L-tyrosine
Analyse K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus jannaschii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDT
- Type
- protein
- Length
- 382 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045…
- Molecule
- L-tyrosine/L-aspartate decarboxylase
- EC
- 4.1.1.11, 4.1.1.25
- UniProt
- Q60358
- Ligands
- EBR, SO4
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · resolution 1.93 · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-tyrosine/L-aspartate decarboxylase (EC 4.1.1.11, 4.1.1.25) | protein | 382 | 47% helix, 13% strand | Q60358 |
Ligands and binding sites
- EBR · [(4Z)-4-[[(Z)-2-(4-hydroxyphenyl) ethylideneamino]methylidene]-6-methyl-5-oxidanyl-1H-pyridin-3-yl]methyl dihydrogen phosphate · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.50 | 0.80 | 25 | EBR |
| 2 | 90 | 0.36 | 0.75 | 19 | empty |
| 3 | 51 | 0.26 | 0.73 | 16 | GOL |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6LDT · K245A mutant of L-tyrosine decarboxylase from methanocaldococcus jannaschii complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q60358 · AlphaFold monomer V2.0 prediction for L-TYROSINE/L-aspartate decarboxylase (Q60358) · a predicted model of the same protein · 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 Q60358
- Elsewhere: RCSB PDB 6LDT · PDBe 6LDT · UniProt Q60358
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