Research workbench
Crystal structure of a photoswitchable GFP-like protein dronpa in the bright-state
Analyse Crystal structure of a photoswitchable GFP-like protein dronpa in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z6Y
- Type
- protein
- Length
- 854 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 0.83
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fluorescent protein dronpa | protein | 214 | 4% helix, 58% strand | Q5TLG6 |
| C, D | Fluorescent protein dronpa | protein | 213 | 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 · 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 | 1128 | 0.83 | 0.85 | 103 | empty |
| 2 | 88 | 0.77 | 0.99 | 29 | GYC |
| 3 | 77 | 0.75 | 0.98 | 26 | GYC |
| 4 | 87 | 0.75 | 0.97 | 29 | GYC |
| 5 | 62 | 0.72 | 0.98 | 21 | GYC |
Interfaces
4 interfaces between chains.
- A–C · 1048 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1043 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 892 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 850 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 2Z6Y · Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state · 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 2Z6Y · PDBe 2Z6Y · UniProt Q5TLG6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.