Research workbench
Multi-bunch pink beam serial crystallography: phycocyanin (one chip)
Analyse Multi-bunch pink beam serial crystallography: phycocyanin (one chip) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MJP
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- P50032, P50033
- Ligands
- CYC
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-phycocyanin alpha chain | protein | 162 | 78% helix, 0% strand | P50032 |
| B | C-phycocyanin beta chain | protein | 172 | 77% helix, 0% strand | P50033 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 3 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 | 136 | 0.61 | 0.85 | 28 | CYC |
| 2 | 207 | 0.57 | 0.79 | 31 | CYC |
| 3 | 52 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1640 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 1 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 5MJP · Multi-bunch pink beam serial crystallography: Phycocyanin (One chip) · the same entry in another collection · chain A against A, TM-score 1.00
- P50032 · AlphaFold monomer V2.0 prediction for C-phycocyanin alpha subunit (P50032) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P50033 · AlphaFold monomer V2.0 prediction for C-phycocyanin beta subunit (P50033) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P50032
- Every structure of UniProt P50033
- Elsewhere: RCSB PDB 5MJP · PDBe 5MJP · UniProt P50032 · UniProt P50033
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