MolNFT v1 · #181055 · protein
LR6 rod linker and scaffolded phycoerythrin beta subunits from the phycobilisome of porphyridium purpureum
7LIZ: “LR6 rod linker and scaffolded phycoerythrin beta subunits from the phycobilisome of porphyridium purpureum”. Electron microscopy, 1 ligand (PEB), 7 pockets (best druggability 0.81). MolNFT v1 #181055 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.