Research workbench
Crystal structure of N-glycosylated human calcitonin receptor extracellular domain in complex with salmon calcitonin (16-32)
Analyse Crystal structure of N-glycosylated human calcitonin receptor extracellular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PFO
- Type
- protein
- Length
- 982 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding PROTEIN,CALCITONIN receptor; Calcitonin
- UniProt
- A0A0A8UN35, P30988, Q92163
- Ligands
- GLC, NAG, NH2, SO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltodextrin-binding PROTEIN,CALCITONIN receptor | protein | 474 | 41% helix, 20% strand | A0A0A8UN35, P30988 |
| C, D | Calcitonin | protein | 17 | 0% helix, 0% strand | Q92163 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.79 | 0.81 | 63 | GLC |
| 2 | 775 | 0.70 | 0.77 | 75 | empty |
| 3 | 310 | 0.70 | 0.83 | 27 | GLC |
| 4 | 106 | 0.59 | 0.86 | 23 | empty |
| 5 | 110 | 0.59 | 0.86 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1134 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1093 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 669 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6PFO · Crystal structure of N-glycosylated human calcitonin receptor extracellular domain in… · the same entry in another collection · chain A against A, TM-score 1.00
- P30988 · AlphaFold monomer V2.0 prediction for calcitonin receptor (P30988) · a predicted model of the same protein · chain B against A, TM-score 0.24
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 A0A0A8UN35
- Every structure of UniProt P30988
- Every structure of UniProt Q92163
- Elsewhere: RCSB PDB 6PFO · PDBe 6PFO · UniProt A0A0A8UN35 · UniProt P30988 · UniProt Q92163
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