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
- 6NBI
- Type
- protein
- Length
- 1,141 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parathyroid HORMONE/PARATHYROID hormone-related peptide receptor; Long-acting parathyroid…
- UniProt
- Q03431, P54311, P63212
- Ligands
- CLR
- Pockets
- 16 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Parathyroid HORMONE/PARATHYROID hormone-related peptide receptor | protein | 369 | 67% helix, 4% strand | Q03431 |
| P | Long-acting parathyroid hormone analog | protein | 30 | 67% helix, 0% strand | — |
| A | Gs protein alpha subunit | protein | 221 | 42% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 6% helix, 45% 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
- CLR · Cholesterol · ligand · 3 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.85 | 0.86 | 77 | empty |
| 2 | 932 | 0.75 | 0.78 | 67 | empty |
| 3 | 444 | 0.74 | 0.83 | 65 | empty |
| 4 | 508 | 0.73 | 0.81 | 54 | empty |
| 5 | 1172 | 0.71 | 0.75 | 77 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2140 Ų buried · 9 hydrogen bonds · protein-protein
- R–P · 1912 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 17 hydrogen bonds · protein-protein
- R–A · 1128 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 999 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6NBI · Cryo-EM structure of parathyroid hormone receptor type 1 in complex with a long-acting… · the same entry in another collection · chain N against N, 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 0.99
- 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 0.95
- 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 0.63
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 6NBI · PDBe 6NBI · UniProt Q03431 · UniProt P54311 · UniProt P63212
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