MolNFT v1 · #155636 · protein
K245A mutant of L-tyrosine decarboxylase from methanocaldococcus jannaschii complexed with a post-decarboxylation quinonoid-like intermediate formed with L-tyrosine
6LDT · L-TYROSINE/L-aspartate decarboxylase: “K245A mutant of L-tyrosine decarboxylase from methanocaldococcus jannaschii complexed with a…”. X-ray diffraction, 2 ligands (EBR, SO4), 3 pockets (best druggability 0.50). MolNFT v1 #155636 on…
- PDB
- 6LDT
- Type
- protein
- Length
- 382 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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