Research workbench
Crystal structure of psilocybe cubensis noncanonical aromatic amino acid decarboxylase
Analyse Crystal structure of psilocybe cubensis noncanonical aromatic amino acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EBN
- Type
- protein
- Length
- 1,919 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non canonical aromatic amino acid decarboxylase
- Ligands
- NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non canonical aromatic amino acid decarboxylase | protein | 961 | 38% helix, 19% strand | — |
| B | Non canonical aromatic amino acid decarboxylase | protein | 958 | 39% helix, 20% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- FMT · Formic acid · additive · 12 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.77 | 0.98 | 25 | empty |
| 2 | 100 | 0.77 | 0.97 | 24 | empty |
| 3 | 779 | 0.77 | 0.81 | 92 | empty |
| 4 | 1129 | 0.76 | 0.79 | 105 | empty |
| 5 | 210 | 0.55 | 0.78 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 8518 Ų buried · 93 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6EBN · Crystal structure of Psilocybe cubensis noncanonical aromatic amino acid decarboxylase · the same entry in another collection · 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
- Elsewhere: RCSB PDB 6EBN · PDBe 6EBN
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