MolNFT v1 · #82795 · protein
N33D mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F)
3VY2: “N33D mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F)”. X-ray diffraction, 1 ligand (FMN), 4 pockets (best druggability 0.59). MolNFT v1 #82795 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VY2
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-binding protein
- UniProt
- Q46604
- Ligands
- FMN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | FMN-binding protein | protein | 122 | 19% helix, 52% strand | Q46604 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.59 | 0.81 | 27 | FMN |
| 2 | 234 | 0.59 | 0.80 | 37 | FMN |
| 3 | 91 | 0.45 | 0.80 | 18 | empty |
| 4 | 67 | 0.33 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3VY2 · N33D mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) · the same entry in another collection · chain A against A, TM-score 1.00
- Q46604 · AlphaFold monomer V2.0 prediction for FMN-binding protein (Q46604) · a predicted model of the same protein · chain B 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 Q46604
- Elsewhere: RCSB PDB 3VY2 · PDBe 3VY2 · UniProt Q46604
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