Research workbench
Structure of C-phycocyanin from arctic pseudanabaena sp. LW0831
Analyse Structure of C-phycocyanin from arctic pseudanabaena sp. LW0831 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TOU
- Type
- protein
- Length
- 2,004 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycocyanin alpha-1 subunit; Phycocyanin beta-1 subunit
- UniProt
- V5NXI0, V5NZF0
- Ligands
- CYC
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, E, I, G, K | Phycocyanin alpha-1 subunit | protein | 162 | 78% helix, 0% strand | V5NXI0 |
| D, B, F, J, H, L | Phycocyanin beta-1 subunit | protein | 172 | 73% helix, 0% strand | V5NZF0 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 18 copies · chains C, B, D, I, A, F, K, E, G, H, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.83 | 0.84 | 113 | CYC |
| 2 | 340 | 0.82 | 0.91 | 39 | CYC |
| 3 | 314 | 0.81 | 0.91 | 36 | CYC |
| 4 | 333 | 0.81 | 0.90 | 38 | CYC |
| 5 | 337 | 0.80 | 0.90 | 40 | CYC |
Interfaces
30 interfaces between chains.
- G–H · 1608 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1599 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1594 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1593 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1584 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 cofactor, 6 modified (phycocyanobilin attachment, nonstandard).
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 V5NXI0
- Every structure of UniProt V5NZF0
- Elsewhere: RCSB PDB 5TOU · PDBe 5TOU · UniProt V5NXI0 · UniProt V5NZF0
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