MolNFT v1 · #158329 · protein
Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2), Y63(3-cly)
6NQL: “Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2), Y63(3-cly)”. X-ray diffraction, 1 ligand (KZ7), 20 pockets (best druggability 0.77). MolNFT v1 #158329 on GenesisL1: 3D structure, binding…
- PDB
- 6NQL
- Type
- protein
- Length
- 1,726 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- KZ7
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, G | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| E, F | Fluorescent protein dronpa | protein | 215 | 4% helix, 58% strand | Q5TLG6 |
| H | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
Ligands and binding sites
- KZ7 · {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(3-chloro-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
- PGE · Triethylene glycol · additive · 3 copies · chains B, C, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.77 | 0.98 | 25 | KZ7 |
| 2 | 89 | 0.76 | 0.98 | 25 | KZ7 |
| 3 | 91 | 0.76 | 0.98 | 28 | KZ7 |
| 4 | 85 | 0.75 | 0.98 | 26 | KZ7 |
| 5 | 84 | 0.75 | 0.97 | 26 | KZ7 |
Interfaces
11 interfaces between chains.
- B–H · 888 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 858 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 216 Ų buried · 0 hydrogen bonds · protein-protein
- B–F · 197 Ų buried · 0 hydrogen bonds · protein-protein
- C–H · 93 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6NQL · 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 6NQL · PDBe 6NQL · UniProt Q5TLG6
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