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Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
Analyse Structural characterization of a blue chromoprotein and its yellow mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IB6
- Type
- protein
- Length
- 1,800 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yellow mutant chromo protein
- UniProt
- A0AQQ8
- Ligands
- QLG, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Yellow mutant chromo protein | protein | 225 | 6% helix, 56% strand | A0AQQ8 |
Ligands and binding sites
- QLG · [(4Z)-2-[(1Z)-4-amino-4-oxobutanimidoyl]-4-(2-methylpropylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl]acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PO4 · Phosphate ion · ion · 16 copies · chains A, B, C, D, E, F, G, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.85 | 0.86 | 99 | PO4 |
| 2 | 1174 | 0.82 | 0.83 | 109 | PO4 |
| 3 | 960 | 0.81 | 0.83 | 100 | empty |
| 4 | 120 | 0.79 | 0.98 | 28 | QLG |
| 5 | 117 | 0.78 | 0.97 | 29 | QLG |
Interfaces
19 interfaces between chains.
- B–C · 1894 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1879 Ų buried · 26 hydrogen bonds · protein-protein
- E–H · 1875 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1872 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 modified, 16 covalent (engineered, covalent ligand).
Compared structures
- 2IB6 · Structural characterization of a blue chromoprotein and its yellow mutant from the sea… · 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 A0AQQ8
- Elsewhere: RCSB PDB 2IB6 · PDBe 2IB6 · UniProt A0AQQ8
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