Research workbench
Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2)- Y63(3-NO2Y)
Analyse Crystal structure of fast switching M159T mutant of fluorescent protein dronpa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NQR
- Type
- protein
- Length
- 1,731 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- KY7
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Fluorescent protein dronpa | protein | 216 | 4% helix, 56% strand | Q5TLG6 |
| B, F | Fluorescent protein dronpa | protein | 216 | 4% helix, 56% strand | Q5TLG6 |
| C | Fluorescent protein dronpa | protein | 217 | 4% helix, 56% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 214 | 4% helix, 57% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 215 | 4% helix, 57% strand | Q5TLG6 |
| G | Fluorescent protein dronpa | protein | 221 | 5% helix, 56% strand | Q5TLG6 |
Ligands and binding sites
- KY7 · {(4Z)-2-[(1S)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-nitrophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.83 | 0.85 | 124 | empty |
| 2 | 111 | 0.78 | 0.97 | 25 | KY7 |
| 3 | 103 | 0.77 | 0.97 | 26 | KY7 |
| 4 | 94 | 0.77 | 0.98 | 28 | KY7 |
| 5 | 90 | 0.76 | 0.98 | 28 | KY7 |
Interfaces
16 interfaces between chains.
- B–E · 1354 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 1281 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1249 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1242 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 843 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 covalent (covalent ligand).
Compared structures
- 6NQR · Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)… · 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 6NQR · PDBe 6NQR · UniProt Q5TLG6
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