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Structure of a K245A mutant of L-tyrosine decarboxylase from methanocaldococcus jannaschii complexed with L-tyr: external aldimine form
Analyse Structure of a K245A mutant of L-tyrosine decarboxylase from methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDS
- 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
- 0PR, SO4
- Pockets
- 4 · best druggability 0.49
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
- 0PR · N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.49 | 0.85 | 20 | empty |
| 2 | 127 | 0.48 | 0.79 | 24 | 0PR |
| 3 | 78 | 0.33 | 0.75 | 20 | empty |
| 4 | 55 | 0.32 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6LDS · Structure of a K245A mutant of L-tyrosine decarboxylase from Methanocaldococcus… · 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 6LDS · PDBe 6LDS · UniProt Q60358
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