Research workbench
Isolation, crystallization, crystal structure analysis and refinement of constitutive C-phycocyanin from the chromatically adapting cyanobacterium fremyella diplosiphon at 1.66 ångströms resolution
Analyse Isolation, crystallization, crystal structure analysis and refinement of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CPC
- Type
- protein
- Length
- 668 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin (alpha subunit); C-phycocyanin (beta subunit)
- UniProt
- P07122, P07119
- Ligands
- CYC
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, K | C-phycocyanin (alpha subunit) | protein | 162 | 79% helix, 0% strand | P07122 |
| B, L | C-phycocyanin (beta subunit) | protein | 172 | 76% helix, 0% strand | P07119 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 6 copies · chains A, B, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.68 | 0.79 | 57 | empty |
| 2 | 97 | 0.64 | 0.89 | 19 | CYC |
| 3 | 105 | 0.63 | 0.88 | 20 | CYC |
| 4 | 283 | 0.60 | 0.79 | 37 | empty |
| 5 | 103 | 0.58 | 0.85 | 20 | CYC |
Interfaces
5 interfaces between chains.
- A–B · 1588 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1585 Ų buried · 12 hydrogen bonds · protein-protein
- A–K · 979 Ų buried · 24 hydrogen bonds · protein-protein
- A–L · 229 Ų buried · 4 hydrogen bonds · protein-protein
- B–K · 226 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 2 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 1CPC · Isolation, crystallization, crystal structure analysis and refinement of constitutive… · the same entry in another collection · chain A against A, TM-score 1.00
- P07122 · AlphaFold monomer V2.0 prediction for C-phycocyanin-1 alpha subunit (P07122) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P07119 · AlphaFold monomer V2.0 prediction for C-phycocyanin-1 beta subunit (P07119) · 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 P07122
- Every structure of UniProt P07119
- Elsewhere: RCSB PDB 1CPC · PDBe 1CPC · UniProt P07122 · UniProt P07119
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