Research workbench
Structure of a. marina phycocyanin contains overlapping isoforms
Analyse Structure of a. marina phycocyanin contains overlapping isoforms in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OOK
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanin, alpha subunit; Phycocyanin, beta subunit
- UniProt
- A8ZMJ4, A8ZMJ5
- Ligands
- CYC
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phycocyanin, alpha subunit | protein | 162 | 78% helix, 0% strand | A8ZMJ4 |
| B | Phycocyanin, beta subunit | protein | 172 | 77% helix, 0% strand | A8ZMJ5 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.62 | 0.88 | 22 | CYC |
| 2 | 172 | 0.56 | 0.80 | 31 | CYC |
| 3 | 54 | 0.30 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1718 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor (phycocyanobilin attachment).
Compared structures
- 5OOK · Structure of A. marina Phycocyanin contains overlapping isoforms · 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 A8ZMJ4
- Every structure of UniProt A8ZMJ5
- Elsewhere: RCSB PDB 5OOK · PDBe 5OOK · UniProt A8ZMJ4 · UniProt A8ZMJ5
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