MolNFT v1 · #184054 · protein
Structure of rslov D109G
7OBZ · Lov protein: “Structure of rslov D109G”. X-ray diffraction, 4 ligands (FMN, SPD, NA), 13 pockets (best druggability 0.75). MolNFT v1 #184054 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OBZ
- Type
- protein
- Length
- 1,049 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lov protein
- UniProt
- M1E1F8
- Ligands
- FMN, SPD, NA, CL
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lov protein | protein | 176 | 47% helix, 21% strand | M1E1F8 |
| B, C, D, F | Lov protein | protein | 175 | 47% helix, 22% strand | M1E1F8 |
| E | Lov protein | protein | 173 | 47% helix, 21% strand | M1E1F8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- SPD · Spermidine · ligand · 5 copies · chains A, B, E
- NA · Sodium ion · metal · 3 copies · chains B, C, D
- CL · Chloride ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.75 | 0.91 | 23 | FMN |
| 2 | 196 | 0.75 | 0.90 | 25 | FMN |
| 3 | 164 | 0.75 | 0.92 | 23 | FMN |
| 4 | 779 | 0.74 | 0.79 | 73 | FMN |
| 5 | 173 | 0.72 | 0.90 | 24 | FMN |
Interfaces
5 interfaces between chains.
- B–C · 1064 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 1053 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 479 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 193 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 129 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7OBZ · Structure of RsLOV D109G · 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 M1E1F8
- Elsewhere: RCSB PDB 7OBZ · PDBe 7OBZ · UniProt M1E1F8
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