Research workbench
Structure of E285D S. cerevisiae FDC1 with prfmn in the hydroxylated form
Analyse Structure of E285D S. cerevisiae FDC1 with prfmn in the hydroxylated form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 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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