MolNFT v1 · #105851 · protein
Crystal structure of ubix, an aromatic acid decarboxylase from the colwellia psychrerythraea 34H
4RHE · 3-octaprenyl-4-hydroxybenzoate carboxy-lyase: “Crystal structure of ubix, an aromatic acid decarboxylase from the colwellia psychrerythraea 34H”. X-ray diffraction, 2 ligands (FMN, SO4), 12 pockets (best druggability 0.82). MolNFT…
- PDB
- 4RHE
- Type
- protein
- Length
- 1,212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
- EC
- 4.1.1.-
- UniProt
- Q489U8
- Ligands
- FMN, SO4
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 202 | 43% helix, 15% strand | Q489U8 |
| B | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 203 | 43% helix, 15% strand | Q489U8 |
| C | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) | protein | 201 | 42% helix, 15% strand | Q489U8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, D, E, B, C, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, F, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.82 | 0.83 | 123 | FMN, SO4 |
| 2 | 293 | 0.74 | 0.87 | 44 | FMN |
| 3 | 798 | 0.72 | 0.78 | 96 | empty |
| 4 | 275 | 0.55 | 0.76 | 24 | empty |
| 5 | 90 | 0.41 | 0.78 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–D · 1605 Ų buried · 22 hydrogen bonds · protein-protein
- C–E · 1551 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 684 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 663 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 646 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4RHE · Crystal structure of UbiX, an aromatic acid decarboxylase from the Colwellia… · 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 Q489U8
- Elsewhere: RCSB PDB 4RHE · PDBe 4RHE · UniProt Q489U8
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