MolNFT v1 · #122195 · protein
Crystal structure of the human calcitonin receptor ectodomain in complex with a truncated salmon calcitonin analogue
5II0: “Crystal structure of the human calcitonin receptor ectodomain in complex with a truncated salmon calcitonin…”. X-ray diffraction, 2 ligands (URE, NA), 4 pockets (best druggability 0.73). MolNFT v1 #122195 on GenesisL1: 3D structure…
- PDB
- 5II0
- Type
- protein
- Length
- 335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calcitonin receptor; Calcitonin
- UniProt
- P30988, Q8QG84
- Ligands
- URE, NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 21% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calcitonin receptor | protein | 99 | 24% helix, 25% strand | P30988 |
| B | Calcitonin receptor | protein | 103 | 22% helix, 23% strand | P30988 |
| C | Calcitonin receptor | protein | 100 | 21% helix, 25% strand | P30988 |
| D, F | Calcitonin | protein | 12 | 0% helix, 0% strand | Q8QG84 |
| E | Calcitonin | protein | 9 | 0% helix, 0% strand | Q8QG84 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 857 | 0.73 | 0.77 | 93 | empty |
| 2 | 168 | 0.73 | 0.90 | 33 | empty |
| 3 | 73 | 0.45 | 0.82 | 17 | empty |
| 4 | 86 | 0.31 | 0.73 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–F · 721 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 658 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 653 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 625 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 497 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 5 modified (disulfide, nonstandard).
Compared structures
- 5II0 · Crystal structure of the human calcitonin receptor ectodomain in complex with a truncated… · the same entry in another collection · chain F against F, TM-score 1.00
- P30988 · AlphaFold monomer V2.0 prediction for calcitonin receptor (P30988) · 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 P30988
- Every structure of UniProt Q8QG84
- Elsewhere: RCSB PDB 5II0 · PDBe 5II0 · UniProt P30988 · UniProt Q8QG84
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