Research workbench
Neurokinin B bound to active human neurokinin 3 receptor in complex with Gq
Analyse Neurokinin B bound to active human neurokinin 3 receptor in complex with Gq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8JBG
- Type
- protein
- Length
- 1,139 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Bos taurus; Homo sapiens; Mus musculus; Rattus norvegicus
- Molecule
- Neuromedin-K receptor (NK3R-pFastbac1); Guanine nucleotide-binding protein G(I)/G(S)/G(T)…
- UniProt
- P54311, P63212, Q9UHF0
- Pockets
- 13 · best druggability 0.81
Structure
electron microscopy · resolution 2.8 · 6 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Neuromedin-K receptor (NK3R-pFastbac1) | protein | 278 | 79% helix, 1% strand | — |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 47% strand | P54311 |
| E | ScFv16 nanobody | protein | 231 | 4% helix, 48% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 55 | 51% helix, 0% strand | P63212 |
| A | Neurokinin-B | protein | 8 | 0% helix, 0% strand | Q9UHF0 |
| C | Guanine nucleotide-binding protein Gq (G324) | protein | 229 | 43% helix, 16% strand | — |
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.81 | 0.86 | 55 | empty |
| 2 | 749 | 0.70 | 0.77 | 74 | empty |
| 3 | 50 | 0.58 | 0.91 | 20 | empty |
| 4 | 297 | 0.57 | 0.77 | 43 | empty |
| 5 | 154 | 0.57 | 0.81 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–G · 2142 Ų buried · 15 hydrogen bonds · protein-protein
- D–C · 1528 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 987 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 760 Ų buried · 6 hydrogen bonds · protein-protein
- E–C · 552 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 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 D against A, TM-score 0.99
- 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 0.66
- Q9UHF0 · AlphaFold monomer V2.0 prediction for tachykinin-3 (Q9UHF0) · a predicted model of the same protein · chain A against A, TM-score 0.52
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 P54311
- Every structure of UniProt P63212
- Every structure of UniProt Q9UHF0
- Elsewhere: RCSB PDB 8JBG · PDBe 8JBG · UniProt P54311 · UniProt P63212 · UniProt Q9UHF0
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