MolNFT v2 · #191662 · protein
Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the P21 space group
7QD2 · Orange carotenoid-binding protein: “Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the P21 space…”. X-ray diffraction at 1.4, 1 ligand (45D), 7 pockets (best druggability 0.87). MolNFT…
- 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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