Research workbench
Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll F-containing cyanobacterium halomicronema hongdechloris
Analyse Characterization of red-shifted phycobiliprotein complexes isolated from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBB
- Type
- protein
- Length
- 1,938 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin subunit alpha-B; Allophycocyanin beta chain
- Ligands
- CYC, SO4
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Allophycocyanin subunit alpha-B | protein | 162 | 79% helix, 0% strand | — |
| B, D, F, H, J, L | Allophycocyanin beta chain | protein | 161 | 78% helix, 0% strand | — |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 12 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- SO4 · Sulfate ion · ion · 42 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.79 | 0.90 | 41 | CYC |
| 2 | 299 | 0.79 | 0.89 | 40 | CYC |
| 3 | 303 | 0.78 | 0.89 | 39 | CYC |
| 4 | 298 | 0.78 | 0.89 | 43 | CYC |
| 5 | 285 | 0.77 | 0.89 | 41 | CYC |
Interfaces
18 interfaces between chains.
- C–D · 1529 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1528 Ų buried · 17 hydrogen bonds · protein-protein
- I–J · 1527 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1521 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1518 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 3JBB · Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll… · 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 3JBB · PDBe 3JBB
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