MolNFT v1 · #57410 · protein
E13Q mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F)
3A6R: “E13Q mutant of FMN-binding protein from desulfovibrio vulgaris (miyazaki F)”. X-ray diffraction, 2 ligands (FMN, CL), 9 pockets (best druggability 0.70). MolNFT v1 #57410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3A6R
- 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, CL
- Pockets
- 9 · best druggability 0.70
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
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.70 | 0.79 | 63 | FMN |
| 2 | 254 | 0.59 | 0.79 | 34 | FMN |
| 3 | 213 | 0.59 | 0.81 | 30 | empty |
| 4 | 201 | 0.57 | 0.80 | 27 | FMN |
| 5 | 204 | 0.57 | 0.79 | 29 | FMN |
Interfaces
5 interfaces between chains.
- C–D · 1250 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1212 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 247 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 101 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3A6R · E13Q 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 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 3A6R · PDBe 3A6R · UniProt Q46604
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