Research workbench
Aspergillus niger ferric acid decarboxylase (fdc) L439G variant in complex with prfmn (purified in the radical form) and phenylpropiolic acid
Analyse Aspergillus niger ferric acid decarboxylase (fdc) L439G variant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R3O
- 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
- A0A3F3RNU4
- Ligands
- JQ8, 4LU, K, MN
- Pockets
- 2 · best druggability 0.83
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 | A0A3F3RNU4 |
Ligands and binding sites
- JQ8 · phenylpropiolic acid · ligand · 3 copies · chains A
- 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.83 | 0.88 | 74 | 4LU, K, JQ8 |
| 2 | 54 | 0.31 | 0.76 | 13 | empty |
Compared structures
- 6R3O · Aspergillus niger ferric acid decarboxylase (Fdc) L439G variant in complex with prFMN… · 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
- Every structure of UniProt A0A3F3RNU4
- Elsewhere: RCSB PDB 6R3O · PDBe 6R3O · UniProt A0A3F3RNU4
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