Research workbench
Light Harvesting complex phycocyanin PC 630, from the cryptophyte Chroomonas sp. M1627
Analyse Light Harvesting complex phycocyanin PC 630, from the cryptophyte Chroomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T7U
- Type
- protein
- Length
- 481 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Chroomonas sp. M1627
- Molecule
- Phycoerythrin alpha subunit L1; Phycoerythrin beta subunit; Phycoerythrin alpha subunit S1
- UniProt
- A0A067XP78, A0A067XP72, A0A067XP68
- Ligands
- CYC, M1V, AX9
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.8 · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phycoerythrin alpha subunit L1 | protein | 81 | 19% helix, 22% strand | A0A067XP78 |
| B | Phycoerythrin beta subunit | protein | 162 | 73% helix, 2% strand | A0A067XP72 |
| C | Phycoerythrin alpha subunit S1 | protein | 70 | 23% helix, 26% strand | A0A067XP68 |
| D | Phycoerythrin beta subunit | protein | 168 | 74% helix, 2% strand | A0A067XP72 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 4 copies · chains A, B, C, D
- M1V · mesobiliverdin IX(alpha) · ligand · 2 copies · chains A, B, C, D
- AX9 · DiCys-(15,16)-Dihydrobiliverdin · ligand · 2 copies · chains A, B, D, C
- GOL · Glycerol · additive · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.83 | 0.86 | 87 | AX9, GOL |
| 2 | 481 | 0.71 | 0.81 | 59 | M1V |
| 3 | 192 | 0.71 | 0.88 | 34 | CYC |
| 4 | 190 | 0.71 | 0.88 | 35 | CYC |
| 5 | 160 | 0.68 | 0.88 | 34 | CYC |
Interfaces
6 interfaces between chains.
- A–B · 2395 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2034 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 833 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 691 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 297 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 4 cofactor, 4 modified (covalent ligand, phycocyanobilin attachment, hydroxylation, 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 A0A067XP78
- Every structure of UniProt A0A067XP72
- Every structure of UniProt A0A067XP68
- Elsewhere: RCSB PDB 7T7U · PDBe 7T7U · UniProt A0A067XP78 · UniProt A0A067XP72 · UniProt A0A067XP68
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.