Research workbench
LR6 rod linker and scaffolded phycoerythrin beta subunits from the phycobilisome of porphyridium purpureum
Analyse LR6 rod linker and scaffolded phycoerythrin beta subunits from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LIZ
- Type
- protein
- Length
- 469 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LR6; B-phycoerythrin beta chain
- UniProt
- A0A5J4YMI8, P11393
- Ligands
- PEB
- Pockets
- 7 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LR6 | protein | 115 | 21% helix, 28% strand | A0A5J4YMI8 |
| B, C | B-phycoerythrin beta chain | protein | 177 | 71% 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.81 | 0.90 | 48 | PEB |
| 2 | 682 | 0.78 | 0.83 | 72 | PEB |
| 3 | 1097 | 0.76 | 0.79 | 79 | PEB |
| 4 | 100 | 0.45 | 0.79 | 24 | empty |
| 5 | 76 | 0.40 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2609 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1538 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 298 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 2 modified (phycoerythrobilin attachment, nonstandard).
Compared structures
- 7LIZ · LR6 rod linker and scaffolded phycoerythrin beta subunits from the phycobilisome of… · 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 A0A5J4YMI8
- Every structure of UniProt P11393
- Elsewhere: RCSB PDB 7LIZ · PDBe 7LIZ · UniProt A0A5J4YMI8 · UniProt P11393
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