MolNFT v1 · #185222 · protein
Cryo-EM structure of bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex
7PL9: “Cryo-EM structure of bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex”. Electron microscopy, 1 ligand (RET), 20 pockets (best druggability 0.87). MolNFT v1 #185222 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PL9
- Type
- protein
- Length
- 4,970 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin
- Ligands
- RET
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Rhodopsin | protein | 994 | 69% helix, 1% strand | — |
Ligands and binding sites
- RET · Retinal · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.87 | 0.88 | 102 | empty |
| 2 | 1172 | 0.86 | 0.87 | 123 | empty |
| 3 | 1162 | 0.85 | 0.86 | 124 | empty |
| 4 | 1163 | 0.85 | 0.86 | 120 | empty |
| 5 | 1037 | 0.85 | 0.86 | 115 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3640 Ų buried · 32 hydrogen bonds · protein-protein
- A–E · 3602 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 3582 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 3580 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 3578 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 cofactor (retinal Schiff base).
Compared structures
- 7PL9 · Cryo-EM structure of Bestrhodopsin (rhodopsin-rhodopsin-bestrophin) complex · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7PL9 · PDBe 7PL9
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