MolNFT v1 · #162257 · protein
Aspergillus niger ferulic acid decarboxylase (fdc) in complex with the covalent adduct formed between prfmn cofactor and cinnamic acid following decarboxylation (INT3)
6R3L · Ferulic acid decarboxylase 1: “Aspergillus niger ferulic acid decarboxylase (fdc) in complex with the covalent adduct formed between prfmn…”. X-ray diffraction, 5 ligands (JSH, BYN, SYN), 5 pockets (best druggability 0.85). MolNFT…
- PDB
- 6R3L
- 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
- JSH, BYN, SYN, K, MN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 500 | 31% helix, 23% strand | A2QHE5 |
Ligands and binding sites
- JSH · prFMN cofactor and cinnamic acid adduct · ligand · chains A
- BYN · hydroxylated prenyl-FMN · ligand · chains A
- SYN · ethenylbenzene · 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
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 | 340 | 0.85 | 0.95 | 40 | K, JSH, BYN, SYN |
| 2 | 231 | 0.56 | 0.78 | 41 | empty |
| 3 | 57 | 0.32 | 0.76 | 13 | empty |
| 4 | 75 | 0.31 | 0.74 | 22 | empty |
| 5 | 53 | 0.24 | 0.72 | 18 | empty |
Compared structures
- 6R3L · Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct… · 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 6R3L · PDBe 6R3L · UniProt A2QHE5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.