Research workbench
Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and G protein
Analyse Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NBF
- Type
- protein
- Length
- 1,148 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Bos taurus; Homo sapiens; Rattus norvegicus; synthetic construct; SYNTHETIC…
- Molecule
- Parathyroid hormone/parathyroid hormone-related peptide receptor; Long-acting parathyroid…
- UniProt
- Q03431, P54311, P63212
- Ligands
- CLR, PLM
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · resolution 3.0 · 6 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Parathyroid hormone/parathyroid hormone-related peptide receptor | protein | 368 | 61% helix, 6% strand | Q03431 |
| P | Long-acting parathyroid hormone analog | protein | 32 | 91% helix, 0% strand | — |
| A | Gs protein alpha subunit | protein | 227 | 47% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 6% helix, 46% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 54% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 126 | 7% helix, 45% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.84 | 0.86 | 79 | empty |
| 2 | 985 | 0.75 | 0.78 | 71 | empty |
| 3 | 657 | 0.75 | 0.81 | 85 | empty |
| 4 | 893 | 0.73 | 0.78 | 62 | empty |
| 5 | 63 | 0.72 | 0.97 | 18 | empty |
Interfaces
7 interfaces between chains.
- R–P · 2162 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 2138 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1545 Ų buried · 16 hydrogen bonds · protein-protein
- A–N · 1025 Ų buried · 7 hydrogen bonds · protein-protein
- R–A · 1005 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6NBF · Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting… · the same entry in another collection · chain R against R, TM-score 1.00
- P54311 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 1.00
- Q03431 · AlphaFold monomer V2.0 prediction for parathyroid HORMONE/PARATHYROID hormone-related… · a predicted model of the same protein · chain R against A, TM-score 0.96
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.67
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 Q03431
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 6NBF · PDBe 6NBF · UniProt Q03431 · UniProt P54311 · UniProt P63212
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