MolNFT v1 · #181056 · protein
Linker 3 and scaffolded phycoerythrin beta subunit from the phycobilisome of porphyridium purpureum
7LJ0: “Linker 3 and scaffolded phycoerythrin beta subunit from the phycobilisome of porphyridium purpureum”. Electron microscopy, 1 ligand (PEB), 2 pockets (best druggability 0.64). MolNFT v1 #181056 on GenesisL1: 3D structure, binding…
- PDB
- 7LJ0
- Type
- protein
- Length
- 172 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linker 3; B-phycoerythrin beta chain
- UniProt
- A0A5J4Z323, P11393
- Ligands
- PEB
- Pockets
- 2 · best druggability 0.64
Structure
electron microscopy · 2 distinct chains · 63% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linker 3 | protein | 27 | 0% helix, 56% strand | A0A5J4Z323 |
| B | B-phycoerythrin beta chain | protein | 145 | 74% helix, 0% strand | P11393 |
Ligands and binding sites
- PEB · Phycoerythrobilin · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.64 | 0.88 | 27 | PEB |
| 2 | 54 | 0.39 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 534 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 7LJ0 · Linker 3 and scaffolded phycoerythrin beta subunit 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 0.97
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 A0A5J4Z323
- Every structure of UniProt P11393
- Elsewhere: RCSB PDB 7LJ0 · PDBe 7LJ0 · UniProt A0A5J4Z323 · UniProt P11393
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