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
- 2Z6Z
- Type
- protein
- Length
- 1,292 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Fluorescent protein dronpa | protein | 216 | 6% helix, 57% strand | Q5TLG6 |
| B | Fluorescent protein dronpa | protein | 215 | 4% helix, 58% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 217 | 4% helix, 57% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 213 | 4% helix, 58% strand | Q5TLG6 |
| F | Fluorescent protein dronpa | protein | 215 | 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
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.84 | 0.85 | 114 | empty |
| 2 | 80 | 0.76 | 0.99 | 26 | GYC |
| 3 | 75 | 0.75 | 0.99 | 27 | GYC |
| 4 | 84 | 0.75 | 0.98 | 27 | GYC |
| 5 | 73 | 0.74 | 0.98 | 24 | GYC |
Interfaces
8 interfaces between chains.
- A–C · 1234 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1069 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 868 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 864 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 856 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 2Z6Z · Crystal structure of a photoswitchable GFP-like protein Dronpa in the bright-state · 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 2Z6Z · PDBe 2Z6Z · UniProt Q5TLG6
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