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Crystal structure of blub-like flavoprotein (YP_001089088.1) from clostridium difficile 630 at 1.74 a resolution
Analyse Crystal structure of blub-like flavoprotein (YP_001089088.1) from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EO8
- Type
- protein
- Length
- 1,314 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blub-like flavoprotein
- UniProt
- Q182R2
- Ligands
- FMN, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Blub-like flavoprotein | protein | 219 | 53% helix, 16% strand | Q182R2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- ACT · Acetate ion · additive · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 7 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.72 | 0.88 | 29 | FMN, ACT, CL |
| 2 | 658 | 0.72 | 0.79 | 56 | empty |
| 3 | 196 | 0.71 | 0.88 | 28 | FMN, ACT, CL |
| 4 | 207 | 0.71 | 0.87 | 27 | ACT, CL, FMN |
| 5 | 210 | 0.69 | 0.87 | 28 | ACT, FMN |
Interfaces
6 interfaces between chains.
- C–D · 3949 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3920 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3910 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 464 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 171 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3EO8 · Crystal structure of BluB-like flavoprotein (YP_001089088.1) from CLOSTRIDIUM DIFFICILE… · 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 Q182R2
- Elsewhere: RCSB PDB 3EO8 · PDBe 3EO8 · UniProt Q182R2
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