Research workbench
Cryo-EM structure of the octameric state of C-phycocyanin from thermoleptolyngbya sp. O-77
Analyse Cryo-EM structure of the octameric 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
- 7EH7
- Type
- protein
- Length
- 2,656 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- A0A0X8WU90, A0A0X8WUE0
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O | C-phycocyanin alpha chain | protein | 160 | 78% helix, 0% strand | A0A0X8WU90 |
| B, D, F, H, J, L, N, P | C-phycocyanin beta chain | protein | 172 | 75% helix, 0% strand | A0A0X8WUE0 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 24 copies · chains A, N, B, C, L, D, E, J, F, G, P, H, I, K, M, O
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 | 955 | 0.84 | 0.86 | 99 | CYC |
| 2 | 631 | 0.84 | 0.89 | 68 | CYC |
| 3 | 1124 | 0.84 | 0.85 | 109 | CYC |
| 4 | 429 | 0.84 | 0.91 | 41 | CYC |
| 5 | 444 | 0.84 | 0.91 | 40 | CYC |
Interfaces
40 interfaces between chains.
- M–N · 1584 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1577 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1572 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1571 Ų buried · 9 hydrogen bonds · protein-protein
- O–P · 1548 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 cofactor, 8 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 7EH7 · Cryo-EM structure of the octameric 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 7EH7 · PDBe 7EH7 · UniProt A0A0X8WU90 · UniProt A0A0X8WUE0
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