Research workbench
Aspergillus niger ferulic acid decarboxylase (fdc) E282Q variant in complex with the covalent adduct formed between prfmn cofactor and pentafluorocinnamic acid (INT2)
Analyse Aspergillus niger ferulic acid decarboxylase (fdc) E282Q variant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R3I
- 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
- JRN, K, MN
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 500 | 30% helix, 23% strand | A2QHE5 |
Ligands and binding sites
- JRN · prFMN cofactor and pentafluorocinnamic acid adduct · 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 | 333 | 0.85 | 0.95 | 38 | JRN |
| 2 | 233 | 0.59 | 0.80 | 43 | empty |
| 3 | 59 | 0.32 | 0.76 | 16 | empty |
| 4 | 80 | 0.31 | 0.73 | 21 | empty |
Compared structures
- 6R3I · Aspergillus niger ferulic acid decarboxylase (Fdc) E282Q variant in complex with the… · 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 6R3I · PDBe 6R3I · UniProt A2QHE5
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