MolNFT v1 · #118752 · protein
Crystal structure of the extracellular domain of human calcium sensing receptor with bound GD3+
5FBH · Extracellular calcium-sensing receptor: “Crystal structure of the extracellular domain of human calcium sensing receptor with bound GD3+”. X-ray diffraction, 6 ligands (BCT, TCR, NAG), 10 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 5FBH
- Type
- protein
- Length
- 942 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular calcium-sensing receptor
- UniProt
- P41180
- Ligands
- BCT, TCR, NAG, MG, GD3, CL
- Pockets
- 10 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Extracellular calcium-sensing receptor | protein | 470 | 36% helix, 20% strand | P41180 |
| A | Extracellular calcium-sensing receptor | protein | 472 | 36% helix, 20% strand | P41180 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 2 copies · chains B, A
- TCR · Cyclomethyltryptophan · ligand · 2 copies · chains B, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- MG · Magnesium ion · metal · 3 copies · chains B, A
- GD3 · Gadolinium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.89 | 0.91 | 130 | BCT, TCR |
| 2 | 310 | 0.75 | 0.87 | 46 | MG |
| 3 | 124 | 0.65 | 0.88 | 21 | BCT |
| 4 | 183 | 0.57 | 0.81 | 22 | empty |
| 5 | 163 | 0.57 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 1843 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 glycan, 6 disulfide, 4 modified (N-glycosylation, disulfide, oxidation).
Compared structures
- 5FBH · Crystal structure of the extracellular domain of human calcium sensing receptor with… · 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 0.98
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 5FBH · PDBe 5FBH · UniProt P41180
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