MolNFT v1 · #189324 · protein
Cryo-EM structure of the non-acylated tirzepatide (LY3298176)-bound human gipr-gs complex
7VAB · Gastric inhibitory polypeptide RECEPTOR,GASTRIC inhibitory…: “Cryo-EM structure of the non-acylated tirzepatide (LY3298176)-bound human gipr-gs complex”. Electron microscopy, 1 ligand (CLR), 12 pockets (best druggability 0.83).…
- PDB
- 7VAB
- Type
- protein
- Length
- 1,077 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gastric inhibitory polypeptide RECEPTOR,GASTRIC inhibitory polypeptide RECEPTOR,GASTRIC…
- UniProt
- P48546, P54311, P63212
- Ligands
- CLR
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Gastric inhibitory polypeptide RECEPTOR,GASTRIC inhibitory polypeptide RECEPTOR,GASTRIC inhibitory polypeptide RECEPTOR,HUMAN glucose-dependent insulinotropic polypeptide receptor | protein | 288 | 78% helix, 0% strand | P48546 |
| P | Non-ACYLATED_TIRZEPATIDE | protein | 27 | 93% helix, 0% strand | — |
| A | Mini-gs | protein | 235 | 47% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 7% helix, 47% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 60% helix, 0% strand | P63212 |
| N | Nonobody-35 | protein | 129 | 2% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 6 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.83 | 0.85 | 82 | empty |
| 2 | 758 | 0.75 | 0.80 | 84 | empty |
| 3 | 883 | 0.74 | 0.78 | 79 | empty |
| 4 | 679 | 0.73 | 0.79 | 72 | empty |
| 5 | 101 | 0.59 | 0.86 | 19 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2271 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1602 Ų buried · 22 hydrogen bonds · protein-protein
- R–P · 1371 Ų buried · 11 hydrogen bonds · protein-protein
- R–A · 1032 Ų buried · 10 hydrogen bonds · protein-protein
- A–N · 858 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 7VAB · Cryo-EM structure of the non-acylated tirzepatide (LY3298176)-bound human GIPR-Gs complex · 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
- P48546 · AlphaFold monomer V2.0 prediction for gastric inhibitory polypeptide receptor (P48546) · a predicted model of the same protein · chain R against A, TM-score 0.91
- 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 P48546
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7VAB · PDBe 7VAB · UniProt P48546 · UniProt P54311 · UniProt P63212
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