MolNFT v2 · #213881 · protein
Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex
8J6P · Guanine nucleotide-binding protein G(i) subunit alpha-1: “Cryo-EM structure of the MK-6892-bound human HCAR2-Gi1 complex”. Electron microscopy at 2.55, 4 ligands (CLR, IX8, NIO), 11 pockets (best druggability 0.82). MolNFT v2…
- PDB
- 8J6P
- Type
- protein
- Length
- 1,151 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.55
- Source
- Homo sapiens; synthetic construct
- Molecule
- Guanine nucleotide-binding protein G(i) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, Q8TDS4
- Ligands
- CLR, IX8, NIO, NAG
- Pockets
- 11 · best druggability 0.82
Structure
electron microscopy · resolution 2.55 · 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 | 225 | 45% helix, 18% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 52% helix, 0% strand | P59768 |
| S | single Fab chain (scFv16) | protein | 234 | 5% helix, 47% strand | — |
| R | Hydroxycarboxylic acid receptor 2 | protein | 295 | 74% helix, 1% strand | Q8TDS4 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains R
- IX8 · 7-methyl-N-[(2R)-1-phenoxypropan-2-yl]-3-(4-propan-2-ylphenyl)pyrazolo[1,5-a]pyrimidine-6-carboxamide · ligand · chains R
- NIO · Nicotinic acid · ligand · chains R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.82 | 0.86 | 61 | empty |
| 2 | 727 | 0.69 | 0.77 | 66 | empty |
| 3 | 99 | 0.62 | 0.88 | 19 | empty |
| 4 | 258 | 0.59 | 0.79 | 42 | empty |
| 5 | 192 | 0.57 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2233 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1223 Ų buried · 21 hydrogen bonds · protein-protein
- A–R · 1071 Ų buried · 11 hydrogen bonds · protein-protein
- A–S · 589 Ų buried · 13 hydrogen bonds · protein-protein
- B–S · 448 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
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 0.96
- 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 0.82
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 Q8TDS4
- Elsewhere: RCSB PDB 8J6P · PDBe 8J6P · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q8TDS4
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