Research workbench
Aspergillus niger ferulic acid decarboxylase (fdc) E282Q variant in complex with the covalent adduct formed between prfmn cofactor and alphafluoro-cinnamic 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
- 6R3G
- 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
- JQQ, K, MN
- Pockets
- 3 · best druggability 0.83
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
- JQQ · [(2~{R},3~{S},4~{S})-5-[(16~{S})-16-[(1~{S})-1-fluoranyl-2-phenyl-ethyl]-11,12,14,14-tetramethyl-5-oxidanyl-3-oxidanylidene-1,4,6,8-tetrazatetracyclo[7.7.1.0^{2,7}.0^{13,17}]heptadeca-2(7),5,9(17),10,12-pentaen-8-yl]-2,3,4-tris(oxidanyl) pentyl] dihydrogen phosphate · 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.83 | 0.88 | 74 | JQQ |
| 2 | 78 | 0.31 | 0.73 | 23 | empty |
| 3 | 59 | 0.31 | 0.75 | 16 | empty |
Compared structures
- 6R3G · 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 6R3G · PDBe 6R3G · UniProt A2QHE5
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