MolNFT v1 · #32598 · protein
The crystal structure of phycocyanin from gracilaria chilensis.
2BV8 · C-phycocyanin alpha subunit: “The crystal structure of phycocyanin from gracilaria chilensis.”. X-ray diffraction, 2 ligands (CYC, PEB), 20 pockets (best druggability 0.83). MolNFT v1 #32598 on GenesisL1: 3D structure, binding sites…
- PDB
- 2BV8
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha subunit; C-phycocyanin beta subunit
- UniProt
- Q6B8L6, Q6B8L7
- Ligands
- CYC, PEB
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, K, M, O | C-phycocyanin alpha subunit | protein | 162 | 78% helix, 0% strand | Q6B8L6 |
| B, D, F, L, N, P | C-phycocyanin beta subunit | protein | 172 | 76% helix, 0% strand | Q6B8L7 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 17 copies · chains A, F, B, C, D, O, E, M, K, P, L, N
- PEB · Phycoerythrobilin · ligand · chains A, B, 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 | 315 | 0.83 | 0.93 | 40 | CYC |
| 2 | 302 | 0.82 | 0.92 | 38 | CYC |
| 3 | 319 | 0.81 | 0.91 | 39 | CYC |
| 4 | 321 | 0.81 | 0.91 | 40 | CYC |
| 5 | 305 | 0.80 | 0.91 | 38 | CYC |
Interfaces
30 interfaces between chains.
- E–F · 1630 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 1630 Ų buried · 18 hydrogen bonds · protein-protein
- O–P · 1626 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1626 Ų buried · 17 hydrogen bonds · protein-protein
- M–N · 1582 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 cofactor, 6 modified (phycocyanobilin attachment, nonstandard, phycoerythrobilin attachment).
Compared structures
- 2BV8 · The crystal structure of Phycocyanin from Gracilaria chilensis. · 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 Q6B8L6
- Every structure of UniProt Q6B8L7
- Elsewhere: RCSB PDB 2BV8 · PDBe 2BV8 · UniProt Q6B8L6 · UniProt Q6B8L7
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