MolNFT v2 · #212172 · protein
Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex
8HN8 · Guanine nucleotide-binding protein G(i) subunit alpha-1: “Cryo-EM structure of ligand histamine-bound Histamine H4 receptor Gi complex”. Electron microscopy at 3.0, 1 ligand (HSM), 15 pockets (best druggability 0.82). MolNFT v2…
- PDB
- 8HN8
- Type
- protein
- Length
- 1,120 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Homo sapiens
- Molecule
- Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P0ABE7, Q9H3N8
- Ligands
- HSM
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · resolution 3.0 · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 218 | 42% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P59768 |
| R | Soluble cytochrome b562, Histamine H4 receptor fusion | protein | 276 | 80% helix, 0% strand | P0ABE7, Q9H3N8 |
| S | Single-chain variable fragment scFv16 | protein | 231 | 4% helix, 45% strand | — |
Ligands and binding sites
- HSM · Histamine · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.82 | 0.84 | 63 | empty |
| 2 | 1031 | 0.76 | 0.78 | 76 | empty |
| 3 | 226 | 0.68 | 0.84 | 39 | HSM |
| 4 | 277 | 0.61 | 0.80 | 45 | empty |
| 5 | 157 | 0.59 | 0.83 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2303 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1169 Ų buried · 9 hydrogen bonds · protein-protein
- A–R · 1102 Ų buried · 4 hydrogen bonds · protein-protein
- A–S · 569 Ų buried · 6 hydrogen bonds · protein-protein
- B–S · 447 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- P62873 · 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
- P59768 · 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 0.90
- Q9H3N8 · AlphaFold monomer V2.0 prediction for histamine H4 receptor (Q9H3N8) · a predicted model of the same protein · chain R against A, TM-score 0.89
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.81
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain R against A, TM-score 0.27
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P0ABE7
- Every structure of UniProt Q9H3N8
- Elsewhere: RCSB PDB 8HN8 · PDBe 8HN8 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P0ABE7 · UniProt Q9H3N8
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