Research workbench
Structure of anabaena (nostoc) sp. pcc 7120 orange carotenoid protein binding canthaxanthin
Analyse Structure of anabaena (nostoc) sp. pcc 7120 orange carotenoid protein binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HGR
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orange carotenoid protein (ocp)
- UniProt
- Q8YSD9
- Ligands
- 45D
- Pockets
- 7 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orange carotenoid protein (ocp) | protein | 315 | 49% helix, 17% strand | Q8YSD9 |
| B | Orange carotenoid protein (ocp) | protein | 309 | 46% helix, 17% strand | Q8YSD9 |
Ligands and binding sites
- 45D · beta,beta-carotene-4,4'-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 805 | 0.87 | 0.90 | 98 | 45D |
| 2 | 610 | 0.87 | 0.91 | 69 | 45D |
| 3 | 181 | 0.68 | 0.87 | 37 | empty |
| 4 | 55 | 0.40 | 0.82 | 18 | empty |
| 5 | 147 | 0.38 | 0.73 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1031 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5HGR · Structure of Anabaena (Nostoc) sp. PCC 7120 Orange Carotenoid Protein 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 Q8YSD9
- Elsewhere: RCSB PDB 5HGR · PDBe 5HGR · UniProt Q8YSD9
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