MolNFT v1 · #176691 · protein
Cryo-EM structure of the compound 2-bound human glp-1 receptor-gs complex
7DUR · Guanine nucleotide-binding protein G(S) subunit alpha…: “Cryo-EM structure of the compound 2-bound human glp-1 receptor-gs complex”. Electron microscopy, 2 ligands (CLR, HNO), 15 pockets (best druggability 0.81). MolNFT v1 #176691…
- PDB
- 7DUR
- Type
- protein
- Length
- 1,126 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P54311, P63212, P43220
- Ligands
- CLR, HNO
- Pockets
- 15 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 235 | 44% helix, 17% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 49% 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 | 371 | 69% helix, 2% 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
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.81 | 0.85 | 57 | empty |
| 2 | 802 | 0.77 | 0.81 | 61 | empty |
| 3 | 849 | 0.73 | 0.78 | 51 | empty |
| 4 | 729 | 0.73 | 0.78 | 59 | empty |
| 5 | 278 | 0.70 | 0.84 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2138 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 24 hydrogen bonds · protein-protein
- A–R · 1099 Ų buried · 16 hydrogen bonds · protein-protein
- A–N · 1083 Ų buried · 20 hydrogen bonds · protein-protein
- B–N · 526 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7DUR · 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 0.83
- 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 0.72
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 7DUR · PDBe 7DUR · UniProt P63092 · UniProt P54311 · UniProt P63212 · UniProt P43220
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