Research workbench
Crystal structure of octameric state of C-phycocyanin from thermoleptolyngbya sp. O-77
Analyse Crystal structure of octameric state of C-phycocyanin from thermoleptolyngbya… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EFV
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- A0A0X8WU90, A0A0X8WUE0
- Ligands
- CYC
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | C-phycocyanin alpha chain | protein | 162 | 77% helix, 0% strand | A0A0X8WU90 |
| B, D | C-phycocyanin beta chain | protein | 172 | 76% helix, 0% strand | A0A0X8WUE0 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.71 | 0.77 | 70 | empty |
| 2 | 83 | 0.61 | 0.88 | 19 | CYC |
| 3 | 77 | 0.59 | 0.88 | 22 | CYC |
| 4 | 171 | 0.59 | 0.82 | 30 | CYC |
| 5 | 162 | 0.58 | 0.82 | 28 | CYC |
Interfaces
5 interfaces between chains.
- A–B · 1619 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1601 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 120 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 2 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 7EFV · Crystal structure of 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 7EFV · PDBe 7EFV · UniProt A0A0X8WU90 · UniProt A0A0X8WUE0
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