MolNFT v1 · #94225 · protein
Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the green-off-state
4HQ9 · Fluorescent protein dronpa: “Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the green-off-state”. X-ray diffraction, 1 ligand (CR8), 13 pockets (best druggability 0.83). MolNFT v1 #94225 on GenesisL1: 3D…
- PDB
- 4HQ9
- 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
- CR8
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% strand | Q5TLG6 |
| B, D | Fluorescent protein dronpa | protein | 215 | 5% helix, 58% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 217 | 5% helix, 57% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% strand | Q5TLG6 |
| F | Fluorescent protein dronpa | protein | 213 | 7% helix, 58% strand | Q5TLG6 |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 6 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, D, E, F
- PG4 · Tetraethylene glycol · additive · 2 copies · chains C, D, F, E
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.83 | 0.85 | 90 | PG4, PEG |
| 2 | 106 | 0.78 | 0.98 | 26 | CR8 |
| 3 | 90 | 0.77 | 0.98 | 22 | CR8 |
| 4 | 90 | 0.77 | 0.98 | 25 | CR8 |
| 5 | 89 | 0.76 | 0.98 | 26 | CR8 |
Interfaces
9 interfaces between chains.
- C–D · 1223 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1062 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 917 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 887 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 870 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 4HQ9 · Crystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the… · 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 4HQ9 · PDBe 4HQ9 · UniProt Q5TLG6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.