MolNFT v1 · #185766 · protein
Structure of the orange carotenoid protein from planktothrix agardhii binding echinenone in the P21 space group
7QD1 · Orange carotenoid-binding protein: “Structure of the orange carotenoid protein from planktothrix agardhii binding echinenone in the P21 space…”. X-ray diffraction, 1 ligand (ECH), 8 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 7QD1
- Type
- protein
- Length
- 621 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orange carotenoid-binding protein
- UniProt
- A0A1J1JHR9
- Ligands
- ECH
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orange carotenoid-binding protein | protein | 311 | 47% helix, 17% strand | A0A1J1JHR9 |
| C | Orange carotenoid-binding protein | protein | 310 | 46% helix, 17% strand | A0A1J1JHR9 |
Ligands and binding sites
- ECH · beta,beta-caroten-4-one · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.87 | 0.92 | 58 | ECH |
| 2 | 715 | 0.86 | 0.89 | 81 | ECH |
| 3 | 137 | 0.75 | 0.94 | 28 | empty |
| 4 | 118 | 0.74 | 0.94 | 26 | empty |
| 5 | 66 | 0.37 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–C · 1205 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7QD1 · Structure of the orange carotenoid protein from Planktothrix agardhii binding echine in… · 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 7QD1 · PDBe 7QD1 · UniProt A0A1J1JHR9
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