Research workbench
Crystal structure of phycocyanin from marine cyanobacterium phormidium rubidum sp. A09DM
Analyse Crystal structure of phycocyanin from marine cyanobacterium phormidium rubidum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YJJ
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha subunit of cyanobacterial phycocyanine protein; Beta subunit of cyanobacterial…
- Ligands
- CYC
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha subunit of cyanobacterial phycocyanine protein | protein | 162 | 79% helix, 0% strand | — |
| B, D | Beta subunit of cyanobacterial phycocyanine protein | protein | 172 | 76% helix, 0% strand | — |
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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.67 | 0.79 | 64 | CYC |
| 2 | 391 | 0.64 | 0.79 | 62 | CYC |
| 3 | 173 | 0.57 | 0.81 | 29 | CYC |
| 4 | 127 | 0.57 | 0.83 | 27 | CYC |
| 5 | 113 | 0.57 | 0.84 | 24 | CYC |
Interfaces
5 interfaces between chains.
- C–D · 1597 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1593 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1028 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 294 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 285 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 2 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 4YJJ · Crystal structure of Phycocyanin from marine cyanobacterium Phormidium rubidum sp. A09DM · 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
- Elsewhere: RCSB PDB 4YJJ · PDBe 4YJJ
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