MolNFT v1 · #155634 · protein
Structure of a K245A mutant of a group II plp dependent decarboxylase from methanocaldococcus jannaschii, in complex with plp
6LDR · L-TYROSINE/L-aspartate decarboxylase: “Structure of a K245A mutant of a group II plp dependent decarboxylase from methanocaldococcus jannaschii, in…”. X-ray diffraction, 3 ligands (PLP, NH4, SO4), 4 pockets (best druggability 0.49).…
- PDB
- 6LDR
- Type
- protein
- Length
- 381 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
- PLP, NH4, 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 | 381 | 47% helix, 13% strand | Q60358 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- NH4 · Ammonium ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 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 | 127 | 0.49 | 0.80 | 22 | PLP |
| 2 | 64 | 0.31 | 0.74 | 21 | GOL |
| 3 | 52 | 0.30 | 0.76 | 15 | empty |
| 4 | 53 | 0.27 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6LDR · Structure of a K245A mutant of a Group II PLP dependent decarboxylase from… · 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 6LDR · PDBe 6LDR · UniProt Q60358
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