Research workbench
Structure of human parathyroid hormone in complex with the extracellular domain of its G-protein-coupled receptor (PTH1R)
Analyse Structure of human parathyroid hormone in complex with the extracellular domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C4M
- Type
- protein
- Length
- 978 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion protein of maltose-binding periplasmic protein and parathyroid HORMONE/PARATHYROID…
- UniProt
- P0AEX9, Q03431, P01270
- Ligands
- GLC, NH2
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusion protein of maltose-binding periplasmic protein and parathyroid HORMONE/PARATHYROID hormone-related peptide receptor | protein | 469 | 41% helix, 20% strand | P0AEX9, Q03431 |
| B | Fusion protein of maltose-binding periplasmic protein and parathyroid HORMONE/PARATHYROID hormone-related peptide receptor | protein | 469 | 42% helix, 21% strand | P0AEX9, Q03431 |
| C, D | Parathyroid hormone | protein | 20 | 90% helix, 0% strand | P01270 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.81 | 0.89 | 42 | empty |
| 2 | 466 | 0.79 | 0.87 | 37 | empty |
| 3 | 411 | 0.74 | 0.84 | 46 | empty |
| 4 | 302 | 0.69 | 0.83 | 35 | GLC |
| 5 | 288 | 0.69 | 0.84 | 35 | GLC |
Interfaces
3 interfaces between chains.
- A–B · 1833 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 981 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 964 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3C4M · Structure of human parathyroid hormone in complex with the extracellular domain of its… · the same entry in another collection · chain A against A, TM-score 1.00
- P01270 · AlphaFold monomer V2.0 prediction for parathyroid hormone (P01270) · a predicted model of the same protein · chain C against A, TM-score 0.69
- Q03431 · AlphaFold monomer V2.0 prediction for parathyroid HORMONE/PARATHYROID hormone-related… · a predicted model of the same protein · chain B against A, TM-score 0.23
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 P0AEX9
- Every structure of UniProt Q03431
- Every structure of UniProt P01270
- Elsewhere: RCSB PDB 3C4M · PDBe 3C4M · UniProt P0AEX9 · UniProt Q03431 · UniProt P01270
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