Research workbench
Structure of the photoacclimated light harvesting complex PC577 from hemiselmis pacifica
Analyse Structure of the photoacclimated light harvesting complex PC577 from hemiselmis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S97
- Type
- protein
- Length
- 478 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phycoerythrin alpha subunit 1; Phycoerythrin beta subunit
- UniProt
- A0A067XP79, A0A067XP89
- Ligands
- CYC, DBV
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phycoerythrin alpha subunit 1 | protein | 63 | 21% helix, 29% strand | A0A067XP79 |
| B, D | Phycoerythrin beta subunit | protein | 176 | 72% helix, 2% strand | A0A067XP89 |
Ligands and binding sites
- CYC · Phycocyanobilin · ligand · 6 copies · chains A, B, C, D
- DBV · 15,16-dihydrobiliverdin · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.78 | 0.80 | 109 | CYC, DBV |
| 2 | 417 | 0.70 | 0.82 | 59 | CYC |
| 3 | 212 | 0.66 | 0.85 | 37 | CYC |
| 4 | 222 | 0.63 | 0.82 | 31 | CYC |
| 5 | 51 | 0.36 | 0.79 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1941 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1931 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 344 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 340 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 121 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 4 covalent (phycocyanobilin attachment, covalent ligand).
Compared structures
- 7S97 · Structure of the Photoacclimated Light Harvesting Complex PC577 from Hemiselmis pacifica · the same entry in another collection · chain B against B, 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 A0A067XP79
- Every structure of UniProt A0A067XP89
- Elsewhere: RCSB PDB 7S97 · PDBe 7S97 · UniProt A0A067XP79 · UniProt A0A067XP89
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