Research workbench
Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the red-on-state
Analyse Crystal structure of a green-to-red photoconvertible dronpa, pcdronpa in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HQC
- Type
- protein
- Length
- 1,295 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- IEY
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Fluorescent protein dronpa | protein | 217 | 5% helix, 57% strand | Q5TLG6 |
| B, C, E | Fluorescent protein dronpa | protein | 215 | 5% helix, 58% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 216 | 5% helix, 57% strand | Q5TLG6 |
Ligands and binding sites
- IEY · {5-hydroxy-4-(4-hydroxybenzyl)-2-[(E)-2-(1H-imidazol-4-yl)ethenyl]-1H-imidazol-1-yl}acetic acid · ligand · 6 copies · chains A, B, C, D, E, F
- PGE · Triethylene glycol · additive · 3 copies · chains A, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, D
- PG4 · Tetraethylene glycol · additive · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.83 | 0.85 | 105 | PGE, PG4 |
| 2 | 82 | 0.76 | 0.99 | 25 | IEY |
| 3 | 77 | 0.76 | 0.99 | 27 | IEY |
| 4 | 82 | 0.76 | 0.98 | 24 | IEY |
| 5 | 79 | 0.76 | 0.99 | 26 | IEY |
Interfaces
9 interfaces between chains.
- E–F · 1313 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1282 Ų buried · 20 hydrogen bonds · protein-protein
- C–E · 907 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 872 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 858 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 4HQC · Crystal structure of a green-to-red photoconvertible DRONPA, pcDRONPA in the red-on-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 4HQC · PDBe 4HQC · UniProt Q5TLG6
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