Research workbench
The 1.7 a crystal structure of dronpa: a photoswitchable green fluorescent protein
Analyse The 1.7 a crystal structure of dronpa: a photoswitchable green fluorescent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IE2
- Type
- protein
- Length
- 1,278 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 212 | 4% helix, 58% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 214 | 4% helix, 58% 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 · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.84 | 0.85 | 115 | empty |
| 2 | 71 | 0.75 | 0.99 | 25 | GYC |
| 3 | 71 | 0.74 | 0.98 | 27 | GYC |
| 4 | 71 | 0.73 | 0.98 | 26 | GYC |
| 5 | 65 | 0.73 | 0.98 | 25 | GYC |
Interfaces
10 interfaces between chains.
- D–F · 967 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 950 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 946 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 909 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 395 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 2IE2 · The 1.7 A crystal structure of Dronpa: a photoswitchable green fluorescent protein · 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 Q5TLG6
- Elsewhere: RCSB PDB 2IE2 · PDBe 2IE2 · UniProt Q5TLG6
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