Research workbench
Crystal structure of R-phycocyanin from polysiphonia at 2.4 a resolution
Analyse Crystal structure of R-phycocyanin from polysiphonia at 2.4 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F99
- Type
- protein
- Length
- 1,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-phycocyanin
- UniProt
- P59858, P59859
- Ligands
- CYC, PEB, BLA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K, M | R-phycocyanin | protein | 162 | 78% helix, 0% strand | P59858 |
| B, L, N | R-phycocyanin | protein | 172 | 76% helix, 0% strand | P59859 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 5 copies · chains B, K, N, L, M
- PEB · Phycoerythrobilin · ligand · 3 copies · chains A, B, K, L, M, N
- BLA · Biliverdine IX alpha · ligand · chains A, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.83 | 0.91 | 38 | CYC |
| 2 | 378 | 0.83 | 0.91 | 39 | BLA |
| 3 | 355 | 0.81 | 0.90 | 38 | CYC |
| 4 | 101 | 0.65 | 0.90 | 22 | CYC |
| 5 | 107 | 0.63 | 0.88 | 21 | CYC |
Interfaces
9 interfaces between chains.
- A–B · 1628 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1617 Ų buried · 12 hydrogen bonds · protein-protein
- M–N · 1613 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 611 Ų buried · 5 hydrogen bonds · protein-protein
- K–N · 609 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 cofactor (phycocyanobilin attachment, phycoerythrobilin attachment, biliverdin attachment).
Compared structures
- 1F99 · Crystal structure of R-phycocyanin from polysiphonia at 2.4 a resolution · the same entry in another collection · chain M against M, TM-score 1.00
- P59858 · AlphaFold monomer V2.0 prediction for R-phycocyanin alpha chain (P59858) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P59859 · AlphaFold monomer V2.0 prediction for R-phycocyanin beta chain (P59859) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P59858
- Every structure of UniProt P59859
- Elsewhere: RCSB PDB 1F99 · PDBe 1F99 · UniProt P59858 · UniProt P59859
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