MolNFT v1 · #105484 · protein
Rational design of enhanced photoresistance in a photoswitchable fluorescent protein
4R6B · Green to red photoconvertible GFP-like protein eosfp: “Rational design of enhanced photoresistance in a photoswitchable fluorescent protein”. X-ray diffraction, 3 ligands (CR8, SO4, SO3), 8 pockets (best druggability 0.82). MolNFT…
- PDB
- 4R6B
- Type
- protein
- Length
- 881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green to red photoconvertible GFP-like protein eosfp
- UniProt
- Q5S6Z9
- Ligands
- CR8, SO4, SO3
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Green to red photoconvertible GFP-like protein eosfp | protein | 220 | 6% helix, 56% strand | Q5S6Z9 |
| B | Green to red photoconvertible GFP-like protein eosfp | protein | 219 | 5% helix, 57% strand | Q5S6Z9 |
| C | Green to red photoconvertible GFP-like protein eosfp | protein | 222 | 3% helix, 56% strand | Q5S6Z9 |
Ligands and binding sites
- CR8 · 2-[1-amino-2-(1H-imidazol-5-yl)ethyl]-1-(carboxymethyl)-4-[(4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-1H-imidazol-5-olate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, C, B, D
- SO3 · Sulfite ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.82 | 0.84 | 78 | empty |
| 2 | 109 | 0.78 | 0.98 | 27 | CR8 |
| 3 | 104 | 0.78 | 0.98 | 29 | CR8 |
| 4 | 95 | 0.76 | 0.98 | 26 | CR8 |
| 5 | 105 | 0.76 | 0.96 | 28 | CR8 |
Interfaces
4 interfaces between chains.
- A–B · 1263 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1246 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1027 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 996 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 4R6B · Rational Design of Enhanced Photoresistance in a Photoswitchable Fluorescent Protein · 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 Q5S6Z9
- Elsewhere: RCSB PDB 4R6B · PDBe 4R6B · UniProt Q5S6Z9
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