Research workbench
Cryo-EM structure of the human glucagon-like peptide-2 receptor-gs protein complex
Analyse Cryo-EM structure of the human glucagon-like peptide-2 receptor-gs protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D68
- Type
- protein
- Length
- 1,070 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P62871, P63212, P01275
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 226 | 43% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 47% strand | P62871 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 51% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 126 | 5% helix, 44% strand | — |
| P | Pro-glucagon | protein | 31 | 84% helix, 0% strand | P01275 |
| R | Glucagon-like peptide 2 receptor | protein | 292 | 72% helix, 0% strand | — |
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 | 750 | 0.82 | 0.85 | 57 | empty |
| 2 | 895 | 0.75 | 0.78 | 107 | empty |
| 3 | 1038 | 0.73 | 0.77 | 73 | empty |
| 4 | 511 | 0.72 | 0.81 | 72 | empty |
| 5 | 172 | 0.68 | 0.87 | 27 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2038 Ų buried · 9 hydrogen bonds · protein-protein
- P–R · 1532 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1471 Ų buried · 18 hydrogen bonds · protein-protein
- A–R · 1027 Ų buried · 7 hydrogen bonds · protein-protein
- A–N · 932 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7D68 · Cryo-EM structure of the human glucagon-like peptide-2 receptor-Gs protein complex · the same entry in another collection · chain R against R, TM-score 1.00
- P62871 · 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 0.83
- 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 0.62
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 P62871
- Every structure of UniProt P63212
- Every structure of UniProt P01275
- Elsewhere: RCSB PDB 7D68 · PDBe 7D68 · UniProt P62871 · UniProt P63212 · UniProt P01275
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