Research workbench
Cryo-EM of human glucagon-like peptide 1 receptor glp-1R in apo form
Analyse Cryo-EM of human glucagon-like peptide 1 receptor glp-1R in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RG9
- Type
- protein
- Length
- 1,246 residues
- Chains
- 6
- 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, P43220
- Pockets
- 19 · best druggability 0.80
Structure
electron microscopy · 6 distinct chains · 31% helix, 28% 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 | 44% helix, 15% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62873 |
| E | Single-chain variable fragment 16 | protein | 232 | 4% helix, 47% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 54% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 128 | 7% helix, 45% strand | — |
| R | Glucagon-like peptide 1 receptor | protein | 268 | 79% helix, 0% strand | P43220 |
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.80 | 0.86 | 55 | empty |
| 2 | 939 | 0.79 | 0.81 | 71 | empty |
| 3 | 904 | 0.75 | 0.78 | 67 | empty |
| 4 | 504 | 0.71 | 0.81 | 57 | empty |
| 5 | 141 | 0.69 | 0.90 | 23 | empty |
Interfaces
8 interfaces between chains.
- B–G · 2140 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1513 Ų buried · 20 hydrogen bonds · protein-protein
- A–R · 1000 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 804 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 548 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 7RG9 · cryo-EM of human Glucagon-like peptide 1 receptor GLP-1R in apo form · 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
- 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 0.94
- 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 0.92
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 P43220
- Elsewhere: RCSB PDB 7RG9 · PDBe 7RG9 · UniProt P62873 · UniProt P59768 · UniProt P43220
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.