Research workbench
Structure of rslov D2 variant
Analyse Structure of rslov D2 variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OB0
- Type
- protein
- Length
- 703 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lov protein
- UniProt
- M1E1F8
- Ligands
- FMN, CA, MG, NA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lov protein | protein | 175 | 47% helix, 21% strand | M1E1F8 |
| B, C, D | Lov protein | protein | 176 | 49% helix, 21% strand | M1E1F8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A, D, B, C
- MG · Magnesium ion · metal · chains B, C
- NA · Sodium ion · metal · chains B
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.77 | 0.79 | 121 | ACT, FMN |
| 2 | 174 | 0.75 | 0.91 | 25 | FMN |
| 3 | 178 | 0.74 | 0.90 | 24 | FMN |
| 4 | 221 | 0.71 | 0.87 | 32 | FMN |
| 5 | 105 | 0.52 | 0.83 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–D · 868 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 332 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 225 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 7OB0 · Structure of RsLOV d2 variant · 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 7OB0 · PDBe 7OB0 · UniProt M1E1F8
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