MolNFT v2 · #180037 · protein
Cryo-EM structure of the compound 2-bound human GLP-1 receptor-Gs complex
7EVM · Guanine nucleotide-binding protein G(s) subunit alpha…: “Cryo-EM structure of the compound 2-bound human GLP-1 receptor-Gs complex”. Electron microscopy at 2.5, 2 ligands (CLR, HNO), 12 pockets (best druggability 0.82). MolNFT v2…
- PDB
- 7EVM
- Type
- protein
- Length
- 1,037 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Bos taurus; Homo sapiens; Rattus norvegicus; synthetic construct
- Molecule
- Guanine nucleotide-binding protein G(s) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P54311, P63212, P43220
- Ligands
- CLR, HNO
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · resolution 2.5 · 5 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 235 | 43% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 48% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 59% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 126 | 7% helix, 45% strand | — |
| R | Glucagon-like peptide 1 receptor | protein | 282 | 80% helix, 0% strand | P43220 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 6 copies · chains R
- HNO · N-tert-butyl-6,7-bis(chloranyl)quinoxalin-2-amine · ligand · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.82 | 0.87 | 56 | empty |
| 2 | 1136 | 0.76 | 0.79 | 76 | empty |
| 3 | 843 | 0.74 | 0.78 | 65 | empty |
| 4 | 531 | 0.67 | 0.77 | 45 | empty |
| 5 | 145 | 0.58 | 0.83 | 29 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2172 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1474 Ų buried · 22 hydrogen bonds · protein-protein
- A–R · 1140 Ų buried · 18 hydrogen bonds · protein-protein
- A–N · 1024 Ų buried · 16 hydrogen bonds · protein-protein
- B–N · 599 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7EVM · Cryo-EM structure of the compound 2-bound human glp-1 receptor-gs complex · the same entry in another collection · chain R against R, 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
- 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 0.97
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.85
- 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 0.74
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 P63092
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Every structure of UniProt P43220
- Elsewhere: RCSB PDB 7EVM · PDBe 7EVM · UniProt P63092 · UniProt P54311 · UniProt P63212 · UniProt P43220
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