MolNFT v1 · #154028 · protein
Crystal structure of a group II pyridoxal dependent decarboxylase, llp-bound form from methanocaldococcus jannaschii at 1.72 a
6JY1 · L-TYROSINE/L-aspartate decarboxylase: “Crystal structure of a group II pyridoxal dependent decarboxylase, llp-bound form from methanocaldococcus…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.35). MolNFT v1…
- PDB
- 6JY1
- Type
- protein
- Length
- 390 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
- SO4
- Pockets
- 4 · best druggability 0.35
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% 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 | 390 | 46% helix, 14% strand | Q60358 |
Ligands and binding sites
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 | 52 | 0.35 | 0.79 | 19 | empty |
| 2 | 61 | 0.33 | 0.76 | 15 | empty |
| 3 | 55 | 0.30 | 0.75 | 15 | empty |
| 4 | 58 | 0.28 | 0.74 | 18 | GOL |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6JY1 · Crystal Structure of a Group II pyridoxal dependent decarboxylase, LLP-bound form 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 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 Q60358
- Elsewhere: RCSB PDB 6JY1 · PDBe 6JY1 · UniProt Q60358
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