Research workbench
CARSP2 and scaffolded phycoerythrin beta subunits from the phycobilisome of porphyridium purpureum
Analyse CARSP2 and scaffolded phycoerythrin beta subunits from the phycobilisome of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LIY
- Type
- protein
- Length
- 435 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CARSP2; B-phycoerythrin beta chain
- UniProt
- A0A5J4YX67, P11393
- Ligands
- PEB
- Pockets
- 7 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CARSP2 | protein | 81 | 9% helix, 35% strand | A0A5J4YX67 |
| B, C | B-phycoerythrin beta chain | protein | 177 | 72% helix, 2% strand | P11393 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.76 | 0.87 | 44 | PEB |
| 2 | 307 | 0.73 | 0.86 | 39 | PEB |
| 3 | 465 | 0.65 | 0.78 | 51 | PEB |
| 4 | 117 | 0.53 | 0.82 | 28 | PEB |
| 5 | 101 | 0.43 | 0.78 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1855 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1522 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 185 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 cofactor, 2 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 7LIY · CaRSP2 and scaffolded phycoerythrin beta subunits from the phycobilisome of Porphyridium… · the same entry in another collection · chain A against A, TM-score 1.00
- P11393 · AlphaFold monomer V2.0 prediction for B-phycoerythrin beta chain (P11393) · a predicted model of the same protein · chain B against A, TM-score 0.81
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 A0A5J4YX67
- Every structure of UniProt P11393
- Elsewhere: RCSB PDB 7LIY · PDBe 7LIY · UniProt A0A5J4YX67 · UniProt P11393
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