Research workbench
Structure of a photobleached state of irisfp under low intensity laser-light
Analyse Structure of a photobleached state of irisfp under low intensity laser-light in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LJD
- Type
- protein
- Length
- 881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Green to red photoconvertible gpf-like protein eosfp
- UniProt
- Q5S6Z9
- Ligands
- CR8, SO4, SO3
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Green to red photoconvertible gpf-like protein eosfp | protein | 220 | 5% helix, 56% strand | Q5S6Z9 |
| B | Green to red photoconvertible gpf-like protein eosfp | protein | 219 | 5% helix, 57% strand | Q5S6Z9 |
| C | Green to red photoconvertible gpf-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 · 16 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
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.81 | 0.83 | 67 | empty |
| 2 | 96 | 0.76 | 0.97 | 30 | CR8 |
| 3 | 99 | 0.75 | 0.97 | 27 | CR8 |
| 4 | 89 | 0.75 | 0.97 | 29 | CR8 |
| 5 | 76 | 0.74 | 0.98 | 27 | CR8 |
Interfaces
4 interfaces between chains.
- A–B · 1206 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1189 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1048 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1046 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent, 7 modified (covalent ligand, oxidation).
Compared structures
- 4LJD · Structure of a photobleached state of IrisFP under low intensity laser-light · 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 4LJD · PDBe 4LJD · UniProt Q5S6Z9
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