MolNFT v1 · #181713 · protein
Asymmetric activation of the calcium sensing receptor homodimer
7M3G · Extracellular calcium-sensing receptor: “Asymmetric activation of the calcium sensing receptor homodimer”. Electron microscopy, 7 ligands (ACE, H43, TRP), 20 pockets (best druggability 0.89). MolNFT v1 #181713 on GenesisL1: 3D…
- PDB
- 7M3G
- Type
- protein
- Length
- 1,639 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular calcium-sensing receptor; Etelcalcetide
- UniProt
- P41180
- Ligands
- ACE, H43, TRP, NAG, CA, NH2, PO4
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular calcium-sensing receptor | protein | 821 | 41% helix, 15% strand | P41180 |
| B | Extracellular calcium-sensing receptor | protein | 804 | 40% helix, 16% strand | P41180 |
| C, D | Etelcalcetide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, A, D
- H43 · 2-[4-[(3S)-3-[[(1R)-1-naphthalen-1-ylethyl]amino]pyrrolidin-1-yl]phenyl]ethanoic acid · ligand · 2 copies · chains A, B
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.89 | 0.91 | 142 | TRP, PO4 |
| 2 | 1056 | 0.82 | 0.83 | 108 | CA |
| 3 | 244 | 0.67 | 0.83 | 26 | H43 |
| 4 | 59 | 0.67 | 0.94 | 18 | empty |
| 5 | 330 | 0.66 | 0.81 | 40 | H43 |
Interfaces
5 interfaces between chains.
- A–B · 3000 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 355 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 330 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 324 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 14 d-amino, 10 glycan, 2 covalent (disulfide, D-amino acid, N-glycosylation, covalent ligand).
Compared structures
- 7M3G · 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 B against A, TM-score 0.80
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 7M3G · PDBe 7M3G · UniProt P41180
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