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Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the P21 space group
Analyse Structure of the orange carotenoid protein from Planktothrix agardhii binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QD2
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.4
- Source
- Planktothrix agardhii
- Molecule
- Orange carotenoid-binding protein
- UniProt
- A0A1J1JHR9
- Ligands
- 45D
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · resolution 1.4 · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orange carotenoid-binding protein | protein | 308 | 48% helix, 17% strand | A0A1J1JHR9 |
| C | Orange carotenoid-binding protein | protein | 306 | 47% helix, 17% strand | A0A1J1JHR9 |
Ligands and binding sites
- 45D · beta,beta-carotene-4,4'-dione · ligand · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.87 | 0.93 | 60 | 45D |
| 2 | 534 | 0.87 | 0.92 | 58 | 45D |
| 3 | 164 | 0.74 | 0.92 | 34 | GOL |
| 4 | 168 | 0.72 | 0.90 | 30 | GOL |
| 5 | 113 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–C · 1150 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7QD2 · Structure of the orange carotenoid protein from planktothrix agardhii binding… · 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 A0A1J1JHR9
- Elsewhere: RCSB PDB 7QD2 · PDBe 7QD2 · UniProt A0A1J1JHR9
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