Research workbench
The crystal structure of allophycocyanin from the red algae gracilaria chilensis
Analyse The crystal structure of allophycocyanin from the red algae gracilaria chilensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TJF
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin alpha subunit; Allophycocyanin beta subunit
- UniProt
- A0A141SEH2, A0A141SEH3
- Ligands
- CYC, NA, CL
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allophycocyanin alpha subunit | protein | 158 | 78% helix, 0% strand | A0A141SEH2 |
| B | Allophycocyanin beta subunit | protein | 160 | 78% helix, 0% strand | A0A141SEH3 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 17 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 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 | 104 | 0.59 | 0.86 | 20 | CYC |
| 2 | 83 | 0.56 | 0.86 | 18 | CYC |
| 3 | 55 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1527 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 5TJF · The crystal structure of Allophycocyanin from the red algae 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 A0A141SEH2
- Every structure of UniProt A0A141SEH3
- Elsewhere: RCSB PDB 5TJF · PDBe 5TJF · UniProt A0A141SEH2 · UniProt A0A141SEH3
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