Research workbench
Structure of E282D A. niger Fdc1 with prFMN in the iminium form
Analyse Structure of E282D A. niger Fdc1 with prFMN in the iminium form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EV7
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.06
- Source
- Aspergillus niger
- Molecule
- Ferulic acid decarboxylase 1
- EC
- 4.1.1.102
- UniProt
- A2QHE5
- Ligands
- 4LU, K, MN
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.06 · 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
- 4LU · 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol · ligand · chains A
- K · Potassium ion · metal · 2 copies · chains A
- MN · Manganese (II) ion · metal · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.85 | 0.95 | 37 | 4LU |
| 2 | 202 | 0.61 | 0.82 | 31 | empty |
| 3 | 58 | 0.31 | 0.75 | 16 | empty |
| 4 | 74 | 0.30 | 0.73 | 21 | empty |
Compared structures
- 6EV7 · Structure of E282D a. niger FDC1 with prfmn in the iminium 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 6EV7 · PDBe 6EV7 · UniProt A2QHE5
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