Research workbench
Room temperature crystal structure of the fast switching M159T mutant of fluorescent protein dronpa
Analyse Room temperature crystal structure of the fast switching M159T mutant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UTS
- Type
- protein
- Length
- 852 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- GYC
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fluorescent protein dronpa | protein | 213 | 3% helix, 58% strand | Q5TLG6 |
Ligands and binding sites
- GYC · [(4Z)-2-[(1R)-1-amino-2-mercaptoethyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.80 | 0.82 | 130 | empty |
| 2 | 93 | 0.78 | 0.99 | 27 | GYC |
| 3 | 86 | 0.76 | 0.98 | 25 | GYC |
| 4 | 88 | 0.76 | 0.98 | 25 | GYC |
| 5 | 86 | 0.75 | 0.97 | 25 | GYC |
Interfaces
4 interfaces between chains.
- C–D · 827 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 599 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 504 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4UTS · Room temperature crystal structure of the fast switching M159T mutant of fluorescent… · 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 4UTS · PDBe 4UTS · UniProt Q5TLG6
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