Research workbench
Crystal structure of E282Q a. niger FDC1 with prfmn in the hydroxylated form
Analyse Crystal structure of E282Q a. niger FDC1 with prfmn in the hydroxylated form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EV5
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferulic acid decarboxylase 1
- EC
- 4.1.1.102
- UniProt
- A2QHE5
- Ligands
- BYN, K, MN, SCN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 500 | 32% helix, 23% strand | A2QHE5 |
Ligands and binding sites
- BYN · hydroxylated prenyl-FMN · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · chains A
- SCN · Thiocyanate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.85 | 0.95 | 38 | BYN, SCN |
| 2 | 185 | 0.58 | 0.81 | 28 | empty |
| 3 | 57 | 0.33 | 0.77 | 16 | empty |
| 4 | 76 | 0.30 | 0.73 | 23 | empty |
| 5 | 58 | 0.30 | 0.75 | 18 | empty |
Compared structures
- 6EV5 · Crystal structure of E282Q A. niger Fdc1 with prFMN in the hydroxylated form · the same entry in another collection · chain A against A, TM-score 1.00
- A2QHE5 · AlphaFold monomer V2.0 prediction for ferulic acid decarboxylase 1 (A2QHE5) · 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 A2QHE5
- Elsewhere: RCSB PDB 6EV5 · PDBe 6EV5 · UniProt A2QHE5
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