Research workbench
Crystal structure of Phormidium rubidum phycocyanin
Analyse Crystal structure of Phormidium rubidum phycocyanin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XWK
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.17
- Source
- Phormidium rubidum A09DM
- Molecule
- Phycocyanin alpha subunit; Phycocyanin beta subunit
- Ligands
- CYC
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · resolution 1.17 · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Phycocyanin alpha subunit | protein | 162 | 78% helix, 0% strand | — |
| BBB | Phycocyanin beta subunit | protein | 172 | 75% helix, 0% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 3 copies · chains AAA, BBB
- EDO · 1,2-ethanediol · additive · 6 copies · chains AAA, BBB
- IMD · Imidazole · additive · 4 copies · chains AAA, BBB
- PEG · Di(hydroxyethyl)ether · additive · chains AAA
- PGE · Triethylene glycol · additive · chains BBB
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.60 | 0.88 | 20 | CYC |
| 2 | 168 | 0.56 | 0.80 | 30 | CYC |
Interfaces
1 interface between chains.
- AAA–BBB · 1707 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 modified (phycocyanobilin attachment, nonstandard).
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6XWK · PDBe 6XWK
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