Research workbench
CARSP1 and scaffolded phycoerythrin beta subunits from the phycobilisome of porphyridium purpureum
Analyse CARSP1 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
- 7LIX
- Type
- protein
- Length
- 721 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CARSP1; B-phycoerythrin beta chain
- UniProt
- A0A5J4YJY8, P11393
- Ligands
- PEB
- Pockets
- 11 · best druggability 0.76
Structure
electron microscopy · 3 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CARSP1 | protein | 205 | 28% helix, 25% strand | A0A5J4YJY8 |
| B | B-phycoerythrin beta chain | protein | 162 | 69% helix, 2% strand | P11393 |
| C, D | B-phycoerythrin beta chain | protein | 177 | 69% helix, 3% strand | P11393 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 405 | 0.76 | 0.85 | 44 | PEB |
| 2 | 386 | 0.76 | 0.86 | 42 | PEB |
| 3 | 239 | 0.73 | 0.87 | 38 | PEB |
| 4 | 130 | 0.59 | 0.85 | 21 | empty |
| 5 | 215 | 0.56 | 0.79 | 33 | PEB |
Interfaces
4 interfaces between chains.
- A–C · 2457 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1955 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1807 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 cofactor, 3 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 7LIX · CaRSP1 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 0.88
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 A0A5J4YJY8
- Every structure of UniProt P11393
- Elsewhere: RCSB PDB 7LIX · PDBe 7LIX · UniProt A0A5J4YJY8 · UniProt P11393
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