Research workbench
Structure of a light-harvesting phycobiliprotein, C-phycocyanin from spirulina platensis at 2.2A resolution
Analyse Structure of a light-harvesting phycobiliprotein, C-phycocyanin from spirulina… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HA7
- Type
- protein
- Length
- 4,008 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-phycocyanin alpha chain; C-phycocyanin beta chain
- UniProt
- P72509, P72508
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W | C-phycocyanin alpha chain | protein | 162 | 78% helix, 0% strand | P72509 |
| B, D, F, H, J, L, N, P, R, T, V, X | C-phycocyanin beta chain | protein | 172 | 77% helix, 0% strand | P72508 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 36 copies · chains A, F, B, G, C, D, K, E, I, L, H, U, J, M, R, N, S, O, P, W, Q, X, T, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.84 | 0.93 | 37 | CYC |
| 2 | 336 | 0.83 | 0.93 | 38 | CYC |
| 3 | 333 | 0.83 | 0.92 | 37 | CYC |
| 4 | 339 | 0.82 | 0.92 | 37 | CYC |
| 5 | 333 | 0.82 | 0.92 | 37 | CYC |
Interfaces
67 interfaces between chains.
- A–B · 1645 Ų buried · 13 hydrogen bonds · protein-protein
- M–N · 1620 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1616 Ų buried · 14 hydrogen bonds · protein-protein
- S–T · 1616 Ų buried · 13 hydrogen bonds · protein-protein
- O–P · 1603 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 cofactor, 12 modified (phycocyanobilin attachment, nonstandard).
Compared structures
- 1HA7 · Structure of a light-harvesting phycobiliprotein, C-phycocyanin from spirulina platensis… · the same entry in another collection · chain E against E, 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 P72509
- Every structure of UniProt P72508
- Elsewhere: RCSB PDB 1HA7 · PDBe 1HA7 · UniProt P72509 · UniProt P72508
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