Research workbench
Structure of a. niger FDC1 with the prenylated-flavin cofactor in the iminium form.
Analyse Structure of a. niger FDC1 with the prenylated-flavin cofactor in the iminium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZA4
- Type
- protein
- Length
- 500 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FDC1
- EC
- 4.1.1.61
- UniProt
- A2QHE5
- Ligands
- 4LU, K, MN
- 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 | FDC1 (EC 4.1.1.61) | 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
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 | 0.94 | 41 | 4LU, K |
| 2 | 204 | 0.54 | 0.78 | 43 | empty |
| 3 | 62 | 0.32 | 0.76 | 14 | empty |
| 4 | 70 | 0.29 | 0.73 | 23 | empty |
| 5 | 53 | 0.25 | 0.73 | 18 | empty |
Compared structures
- 4ZA4 · Structure of A. niger Fdc1 with the prenylated-flavin cofactor 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 4ZA4 · PDBe 4ZA4 · UniProt A2QHE5
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