Research workbench
Cryo-EM structure of the compound 2 and glp-1-bound human glp-1 receptor-gs complex
Analyse Cryo-EM structure of the compound 2 and glp-1-bound human glp-1 receptor-gs… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DUQ
- Type
- protein
- Length
- 1,174 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon-like peptide 1; Glucagon-like peptide 1 receptor; Guanine nucleotide-binding…
- UniProt
- P01275, P43220, P63092, P54311, P63212
- Ligands
- CLR, HNO
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Glucagon-like peptide 1 | protein | 30 | 90% helix, 0% strand | P01275 |
| R | Glucagon-like peptide 1 receptor | protein | 384 | 65% helix, 6% strand | P43220 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 240 | 46% helix, 16% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 48% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 50% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 126 | 7% helix, 44% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 7 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.82 | 0.87 | 56 | empty |
| 2 | 953 | 0.79 | 0.81 | 65 | empty |
| 3 | 722 | 0.70 | 0.77 | 50 | empty |
| 4 | 344 | 0.69 | 0.82 | 50 | empty |
| 5 | 68 | 0.60 | 0.90 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2232 Ų buried · 23 hydrogen bonds · protein-protein
- P–R · 1795 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1546 Ų buried · 26 hydrogen bonds · protein-protein
- R–A · 1134 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 1005 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7DUQ · Cryo-EM structure of the compound 2 and GLP-1-bound human GLP-1 receptor-Gs complex · the same entry in another collection · chain N against N, 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
- P01275 · AlphaFold monomer V2.0 prediction for pro-glucagon (P01275) · a predicted model of the same protein · chain P against A, TM-score 0.82
- 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 0.79
- 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 0.70
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 P01275
- Every structure of UniProt P43220
- Every structure of UniProt P63092
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7DUQ · PDBe 7DUQ · UniProt P01275 · UniProt P43220 · UniProt P63092 · UniProt P54311 · UniProt P63212
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