MolNFT v1 · #94224 · protein
Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the green-on-state
4HQ8 · Fluorescent protein dronpa: “Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the green-on-state”. X-ray diffraction, 1 ligand (CR8), 15 pockets (best druggability 0.83). MolNFT v1 #94224 on GenesisL1: 3D…
- PDB
- 4HQ8
- Type
- protein
- Length
- 1,296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- CR8
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein dronpa | protein | 217 | 4% helix, 57% strand | Q5TLG6 |
| B | Fluorescent protein dronpa | protein | 217 | 5% helix, 57% strand | Q5TLG6 |
| C, D | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 214 | 4% helix, 58% strand | Q5TLG6 |
| F | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% 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
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, C, F, D, E
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, F
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.83 | 0.85 | 110 | empty |
| 2 | 87 | 0.78 | 0.99 | 25 | CR8 |
| 3 | 81 | 0.76 | 0.99 | 24 | CR8 |
| 4 | 85 | 0.75 | 0.97 | 27 | CR8 |
| 5 | 82 | 0.75 | 0.98 | 25 | CR8 |
Interfaces
8 interfaces between chains.
- C–F · 1367 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1295 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 869 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 868 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 833 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 4HQ8 · 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 4HQ8 · PDBe 4HQ8 · UniProt Q5TLG6
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