MolNFT v1 · #181711 · protein
Asymmetric activation of the calcium sensing receptor homodimer
7M3E · Extracellular calcium-sensing receptor: “Asymmetric activation of the calcium sensing receptor homodimer”. Electron microscopy, 5 ligands (YP1, TRP, NAG), 20 pockets (best druggability 0.89). MolNFT v1 #181711 on GenesisL1: 3D…
- PDB
- 7M3E
- Type
- protein
- Length
- 1,622 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular calcium-sensing receptor
- UniProt
- P41180
- Ligands
- YP1, TRP, NAG, CA, PO4
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular calcium-sensing receptor | protein | 810 | 39% helix, 15% strand | P41180 |
| B | Extracellular calcium-sensing receptor | protein | 812 | 40% helix, 15% strand | P41180 |
Ligands and binding sites
- YP1 · 2-chloro-6-[(2R)-2-hydroxy-3-{[2-methyl-1-(naphthalen-2-yl)propan-2-yl]amino}propoxy]benzonitrile · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.89 | 0.90 | 110 | TRP |
| 2 | 971 | 0.80 | 0.82 | 94 | CA |
| 3 | 415 | 0.75 | 0.84 | 47 | YP1 |
| 4 | 457 | 0.73 | 0.82 | 50 | YP1 |
| 5 | 205 | 0.66 | 0.84 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2899 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 7M3E · Asymmetric Activation of the Calcium Sensing Receptor Homodimer · the same entry in another collection · chain A against A, TM-score 1.00
- P41180 · AlphaFold monomer V2.0 prediction for extracellular calcium-sensing receptor (P41180) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P41180
- Elsewhere: RCSB PDB 7M3E · PDBe 7M3E · UniProt P41180
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