Research workbench
Bright-state structure of the reversibly switchable fluorescent protein dronpa
Analyse Bright-state structure of the reversibly switchable fluorescent protein dronpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IOV
- Type
- protein
- Length
- 871 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| B | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 220 | 5% helix, 56% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 219 | 6% helix, 57% strand | Q5TLG6 |
Ligands and binding sites
- GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.85 | 0.87 | 133 | empty |
| 2 | 77 | 0.75 | 0.98 | 27 | GYC |
| 3 | 74 | 0.74 | 0.98 | 26 | GYC |
| 4 | 74 | 0.73 | 0.97 | 27 | GYC |
| 5 | 73 | 0.72 | 0.97 | 27 | GYC |
Interfaces
6 interfaces between chains.
- A–B · 923 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 888 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 564 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 383 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 377 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2IOV · Bright-state structure of the reversibly switchable fluorescent protein Dronpa · the same entry in another collection · chain B against B, 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 Q5TLG6
- Elsewhere: RCSB PDB 2IOV · PDBe 2IOV · UniProt Q5TLG6
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