Research workbench
L122E mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F)
Analyse L122E mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WLK
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-binding protein
- UniProt
- Q46604
- Ligands
- FMN
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | FMN-binding protein | protein | 122 | 18% helix, 50% strand | Q46604 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.59 | 0.81 | 28 | FMN |
| 2 | 197 | 0.57 | 0.80 | 28 | FMN |
| 3 | 172 | 0.56 | 0.81 | 29 | FMN |
| 4 | 180 | 0.55 | 0.80 | 29 | FMN |
| 5 | 64 | 0.46 | 0.83 | 18 | empty |
Interfaces
2 interfaces between chains.
- C–D · 1218 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1135 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1WLK · L122E mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) · the same entry in another collection · chain D against D, TM-score 1.00
- Q46604 · AlphaFold monomer V2.0 prediction for FMN-binding protein (Q46604) · a predicted model of the same protein · chain D 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 Q46604
- Elsewhere: RCSB PDB 1WLK · PDBe 1WLK · UniProt Q46604
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