MolNFT v1 · #148048 · protein
Structure of E285D S. cerevisiae FDC1 with prfmn in the hydroxylated form
6EVF · Ferulic acid decarboxylase 1: “Structure of E285D S. cerevisiae FDC1 with prfmn in the hydroxylated form”. X-ray diffraction, 3 ligands (4LU, MN, K), 20 pockets (best druggability 0.85). MolNFT v1 #148048 on GenesisL1: 3D structure…
- PDB
- 6EVF
- Type
- protein
- Length
- 2,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferulic acid decarboxylase 1
- EC
- 4.1.1.102
- UniProt
- Q03034
- Ligands
- 4LU, MN, K
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 503 | 33% helix, 24% strand | Q03034 |
| B | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 502 | 32% helix, 24% strand | Q03034 |
| C | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 500 | 33% helix, 23% strand | Q03034 |
| D | Ferulic acid decarboxylase 1 (EC 4.1.1.102) | protein | 501 | 32% helix, 23% strand | Q03034 |
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 · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.85 | 0.87 | 100 | empty |
| 2 | 314 | 0.85 | 0.95 | 38 | 4LU |
| 3 | 307 | 0.85 | 0.95 | 37 | 4LU |
| 4 | 338 | 0.84 | 0.94 | 37 | 4LU, K |
| 5 | 302 | 0.84 | 0.94 | 37 | 4LU, K |
Interfaces
3 interfaces between chains.
- A–B · 3545 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 918 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 891 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6EVF · Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxylated form · the same entry in another collection · chain D against D, TM-score 1.00
- Q03034 · AlphaFold monomer V2.0 prediction for ferulic acid decarboxylase 1 (Q03034) · a predicted model of the same protein · chain B 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 Q03034
- Elsewhere: RCSB PDB 6EVF · PDBe 6EVF · UniProt Q03034
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