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3.3 ångström phase-plate cryo-EM structure of a biased agonist-bound human glp-1 receptor-gs complex
Analyse 3.3 ångström phase-plate cryo-EM structure of a biased agonist-bound human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B3J
- Type
- protein
- Length
- 1,129 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon-like peptide 1 receptor; Exendin-P5; Guanine nucleotide-binding protein G(S)…
- UniProt
- P43220, P63092, P62873, P59768
- Pockets
- 15 · best druggability 0.85
Structure
electron microscopy · 6 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Glucagon-like peptide 1 receptor | protein | 380 | 71% helix, 2% strand | P43220 |
| P | Exendin-P5 | protein | 33 | 85% helix, 0% strand | — |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 195 | 45% helix, 21% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 61% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 126 | 7% helix, 44% strand | — |
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 | 802 | 0.85 | 0.87 | 72 | empty |
| 2 | 887 | 0.75 | 0.78 | 68 | empty |
| 3 | 835 | 0.74 | 0.79 | 58 | empty |
| 4 | 266 | 0.60 | 0.79 | 28 | empty |
| 5 | 52 | 0.59 | 0.91 | 17 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2241 Ų buried · 12 hydrogen bonds · protein-protein
- R–P · 1996 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1461 Ų buried · 15 hydrogen bonds · protein-protein
- R–A · 1000 Ų buried · 6 hydrogen bonds · protein-protein
- A–N · 917 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6B3J · 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bound human GLP-1… · the same entry in another collection · chain N against N, 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 0.92
- 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 0.86
- 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 0.82
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 P43220
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6B3J · PDBe 6B3J · UniProt P43220 · UniProt P63092 · UniProt P62873 · UniProt P59768
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