Research workbench
Crystal structure of the active form of human calcium-sensing receptor extracellular domain
Analyse Crystal structure of the active form 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
- 5K5S
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular calcium-sensing receptor
- UniProt
- P41180
- Ligands
- TRP, NAG, CA, PO4
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular calcium-sensing receptor | protein | 531 | 30% helix, 20% strand | P41180 |
| B | Extracellular calcium-sensing receptor | protein | 537 | 29% helix, 22% strand | P41180 |
Ligands and binding sites
- TRP · Tryptophan · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.89 | 0.91 | 143 | TRP, PO4, CA |
| 2 | 665 | 0.80 | 0.85 | 75 | CA |
| 3 | 148 | 0.63 | 0.85 | 21 | empty |
| 4 | 171 | 0.62 | 0.84 | 21 | empty |
| 5 | 228 | 0.59 | 0.80 | 28 | PO4 |
Interfaces
1 interface between chains.
- A–B · 2826 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5K5S · Crystal structure of the active form of human calcium-sensing receptor extracellular… · 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 0.97
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 5K5S · PDBe 5K5S · UniProt P41180
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