Research workbench
Semi-rational engineering of a green-emitting coral fluorescent protein into an efficient highlighter.
Analyse Semi-rational engineering of a green-emitting coral fluorescent protein into an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XSS
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein
- UniProt
- Q53UG7
- Ligands
- DYG, MG, NA
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluorescent protein | protein | 223 | 4% helix, 55% strand | Q53UG7 |
| B | Fluorescent protein | protein | 224 | 4% helix, 55% strand | Q53UG7 |
Ligands and binding sites
- DYG · (3S)-3-amino-3-[(4Z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.74 | 0.98 | 26 | DYG |
| 2 | 68 | 0.74 | 0.98 | 25 | DYG |
| 3 | 123 | 0.50 | 0.81 | 31 | empty |
| 4 | 133 | 0.49 | 0.79 | 26 | empty |
| 5 | 209 | 0.48 | 0.75 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1XSS · Semi-rational engineering of a green-emitting coral fluorescent protein into an efficient… · 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 Q53UG7
- Elsewhere: RCSB PDB 1XSS · PDBe 1XSS · UniProt Q53UG7
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