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Structure of light harvesting complex of allophycocyanin alpha and beta CHAINS/CORE-linker complex AP*LC7.8
Analyse Structure of light harvesting complex of allophycocyanin alpha and beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1B33
- Type
- protein
- Length
- 2,060 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allophycocyanin, alpha chain; Allophycocyanin, beta chain; Phycobilisome 7.8 kd linker…
- UniProt
- P00315, P00318, P20116
- Ligands
- CYC, BLA, BO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, H, J, L | Allophycocyanin, alpha chain | protein | 160 | 78% helix, 0% strand | P00315 |
| B, D, F, I, K, M | Allophycocyanin, beta chain | protein | 161 | 77% helix, 0% strand | P00318 |
| N, O | Phycobilisome 7.8 kd linker polypeptide | protein | 67 | 25% helix, 31% strand | P20116 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 10 copies · chains B, C, D, N, E, F, H, M, I, O, J, K, L
- BLA · Biliverdine IX alpha · ligand · 2 copies · chains A, F, B, N
- BO4 · Borate ion · ion · 4 copies · chains C, E, J, 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 | 819 | 0.78 | 0.82 | 95 | CYC |
| 2 | 1192 | 0.78 | 0.80 | 120 | CYC |
| 3 | 261 | 0.78 | 0.90 | 40 | BLA |
| 4 | 347 | 0.78 | 0.88 | 49 | CYC |
| 5 | 279 | 0.77 | 0.89 | 41 | CYC |
Interfaces
35 interfaces between chains.
- H–I · 1538 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1505 Ų buried · 17 hydrogen bonds · protein-protein
- L–M · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1495 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 1482 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 6 modified (phycocyanobilin attachment, nonstandard, biliverdin attachment).
Compared structures
- 1B33 · Structure of light harvesting complex of allophycocyanin alpha and beta… · the same entry in another collection · chain O against O, 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 P00315
- Every structure of UniProt P00318
- Every structure of UniProt P20116
- Elsewhere: RCSB PDB 1B33 · PDBe 1B33 · UniProt P00315 · UniProt P00318 · UniProt P20116
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