Research workbench
Cryo-EM of human glucagon-like peptide 1 receptor glp-1R bound to tirzepatide
Analyse Cryo-EM of human glucagon-like peptide 1 receptor glp-1R bound to tirzepatide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RGP
- Type
- protein
- Length
- 1,383 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-3, isoform gnas-2 of guanine…
- UniProt
- P08754, P63092, P62873, P59768, P43220
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-3, isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 216 | 44% helix, 16% strand | P08754, P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 47% strand | P62873 |
| E | Single-chain variable fragment 16 | protein | 232 | 3% helix, 46% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 51% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 43% strand | — |
| P | Tirzepatide | protein | 31 | 87% helix, 0% strand | — |
| R | Glucagon-like peptide 1 receptor | protein | 378 | 60% helix, 2% strand | P43220 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.81 | 0.86 | 53 | empty |
| 2 | 893 | 0.78 | 0.81 | 88 | empty |
| 3 | 1010 | 0.77 | 0.79 | 63 | empty |
| 4 | 170 | 0.70 | 0.89 | 27 | empty |
| 5 | 407 | 0.65 | 0.79 | 52 | empty |
Interfaces
9 interfaces between chains.
- B–G · 2056 Ų buried · 14 hydrogen bonds · protein-protein
- P–R · 1677 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1478 Ų buried · 17 hydrogen bonds · protein-protein
- A–R · 1069 Ų buried · 14 hydrogen bonds · protein-protein
- A–N · 905 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 7RGP · cryo-EM of human Glucagon-like peptide 1 receptor GLP-1R bound to tirzepatide · 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
- P43220 · AlphaFold monomer V2.0 prediction for glucagon-like peptide 1 receptor (P43220) · a predicted model of the same protein · chain R against A, TM-score 0.83
- P08754 · 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 0.74
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 P08754
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P43220
- Elsewhere: RCSB PDB 7RGP · PDBe 7RGP · UniProt P08754 · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt P43220
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.