Research workbench
Crystal structure of the extracellular domain of human calcium sensing receptor
Analyse Crystal structure of the extracellular domain of human calcium sensing receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FBK
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular calcium-sensing receptor
- UniProt
- P41180
- Ligands
- TCR, BCT, NAG, MG, CL
- Pockets
- 8 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular calcium-sensing receptor | protein | 487 | 37% helix, 20% strand | P41180 |
| B | Extracellular calcium-sensing receptor | protein | 467 | 37% helix, 20% strand | P41180 |
Ligands and binding sites
- TCR · Cyclomethyltryptophan · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1013 | 0.89 | 0.91 | 152 | TCR, CL, BCT |
| 2 | 318 | 0.76 | 0.88 | 47 | MG |
| 3 | 132 | 0.61 | 0.86 | 22 | empty |
| 4 | 344 | 0.60 | 0.77 | 41 | empty |
| 5 | 162 | 0.57 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2021 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide, 4 modified (N-glycosylation, disulfide, oxidation).
Compared structures
- 5FBK · Crystal structure of the extracellular domain of human calcium sensing receptor · 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 0.98
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 5FBK · PDBe 5FBK · UniProt P41180
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