Research workbench
Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2), Y63(3-bry)
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
- 6NQN
- Type
- protein
- Length
- 1,737 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- KZ4
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein dronpa | protein | 218 | 4% helix, 57% strand | Q5TLG6 |
| B, F, H | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| C, G | Fluorescent protein dronpa | protein | 218 | 4% helix, 57% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 220 | 4% helix, 56% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 215 | 4% helix, 58% strand | Q5TLG6 |
Ligands and binding sites
- KZ4 · {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-bromo-4-hydroxyphenyl)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
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.82 | 0.86 | 93 | empty |
| 2 | 92 | 0.77 | 0.98 | 24 | KZ4 |
| 3 | 94 | 0.76 | 0.98 | 26 | KZ4 |
| 4 | 86 | 0.76 | 0.98 | 28 | KZ4 |
| 5 | 93 | 0.76 | 0.97 | 25 | KZ4 |
Interfaces
14 interfaces between chains.
- D–F · 1374 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1322 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1215 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 865 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6NQN · 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 6NQN · PDBe 6NQN · UniProt Q5TLG6
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