MolNFT v1 · #186371 · protein
Cryo-EM structure of human gastric inhibitory polypeptide receptor gipr bound to tirzepatide
7RBT · Isoform gnas-2 of guanine nucleotide-binding protein G(S)…: “Cryo-EM structure of human gastric inhibitory polypeptide receptor gipr bound to tirzepatide”. Electron microscopy, 1 ligand (41Y), 19 pockets (best druggability 0.81).…
- PDB
- 7RBT
- Type
- protein
- Length
- 1,386 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short…
- UniProt
- P62873, P59768, P48546
- Ligands
- 41Y
- Pockets
- 19 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 220 | 42% helix, 13% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 42% strand | P62873 |
| E | Single-chain variable fragment 16 | protein | 232 | 3% helix, 40% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 51% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 41% strand | — |
| P | Tirzepatide | protein | 32 | 84% helix, 0% strand | — |
| R | Gastric inhibitory polypeptide receptor | protein | 378 | 62% helix, 3% strand | P48546 |
Ligands and binding sites
- 41Y · 2-fluoro-4-[(1R)-6-methoxy-1-methyl-2-{(1S)-1-[4-(propan-2-yl)phenyl]ethyl}-1,2,3,4-tetrahydroisoquinolin-5-yl]-6-[(2-methylpropyl) amino]phenol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.81 | 0.85 | 52 | empty |
| 2 | 896 | 0.74 | 0.78 | 75 | empty |
| 3 | 855 | 0.74 | 0.78 | 63 | empty |
| 4 | 581 | 0.72 | 0.80 | 64 | empty |
| 5 | 517 | 0.72 | 0.81 | 72 | empty |
Interfaces
9 interfaces between chains.
- B–G · 2089 Ų buried · 17 hydrogen bonds · protein-protein
- P–R · 1759 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1484 Ų buried · 16 hydrogen bonds · protein-protein
- A–R · 962 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 848 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 7RBT · cryo-EM structure of human Gastric inhibitory polypeptide receptor GIPR bound to… · the same entry in another collection · chain R against R, TM-score 1.00
- 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 0.91
- 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 0.77
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P48546
- Elsewhere: RCSB PDB 7RBT · PDBe 7RBT · UniProt P62873 · UniProt P59768 · UniProt P48546
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.