Research workbench
Cryo-EM structure of the hexameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77
Analyse Cryo-EM structure of the hexameric state of C-phycocyanin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EH8
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.06
- Source
- Leptolyngbya sp. O-77
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- A0A0X8WU90, A0A0X8WUE0
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.06 · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | C-phycocyanin alpha chain | protein | 162 | 77% helix, 0% strand | A0A0X8WU90 |
| B, D, F, H, J, L | C-phycocyanin beta chain | protein | 172 | 75% helix, 0% strand | A0A0X8WUE0 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 18 copies · chains A, L, B, C, H, D, E, F, G, J, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.84 | 0.92 | 40 | CYC |
| 2 | 406 | 0.84 | 0.92 | 38 | CYC |
| 3 | 399 | 0.83 | 0.91 | 38 | CYC |
| 4 | 393 | 0.83 | 0.91 | 40 | CYC |
| 5 | 413 | 0.83 | 0.91 | 40 | CYC |
Interfaces
30 interfaces between chains.
- I–J · 1598 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1596 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1592 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1591 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1590 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 7EH8 · Cryo-EM structure of the hexameric state of C-phycocyanin from thermoleptolyngbya sp. O-77 · 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 A0A0X8WU90
- Every structure of UniProt A0A0X8WUE0
- Elsewhere: RCSB PDB 7EH8 · PDBe 7EH8 · UniProt A0A0X8WU90 · UniProt A0A0X8WUE0
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