Research workbench
Structural basis of ligand selectivity conferred by the human glucose- dependent insulinotropic polypeptide receptor
Analyse Structural basis of ligand selectivity conferred by the human glucose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DTY
- Type
- protein
- Length
- 1,156 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human glucose-dependent insulinotropic polypeptide receptor; Gastric inhibitory…
- UniProt
- P09681, P04896, P54311, P63212
- Ligands
- CLR
- Pockets
- 17 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Human glucose-dependent insulinotropic polypeptide receptor | protein | 367 | 68% helix, 4% strand | — |
| P | Gastric inhibitory polypeptide | protein | 30 | 90% helix, 0% strand | P09681 |
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 232 | 50% helix, 17% strand | P04896 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 7% helix, 48% strand | P54311 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 54% helix, 0% strand | P63212 |
| N | Nanobody-35 | protein | 129 | 7% helix, 44% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 6 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.83 | 0.86 | 79 | empty |
| 2 | 914 | 0.79 | 0.82 | 78 | empty |
| 3 | 881 | 0.76 | 0.79 | 61 | empty |
| 4 | 249 | 0.68 | 0.84 | 37 | empty |
| 5 | 66 | 0.65 | 0.93 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2339 Ų buried · 16 hydrogen bonds · protein-protein
- R–P · 2017 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1532 Ų buried · 25 hydrogen bonds · protein-protein
- R–A · 1205 Ų buried · 14 hydrogen bonds · protein-protein
- A–N · 991 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7DTY · Structural basis of ligand selectivity conferred by the human glucose-dependent… · 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
- P09681 · AlphaFold monomer V2.0 prediction for gastric inhibitory polypeptide (P09681) · a predicted model of the same protein · chain P against A, TM-score 0.85
- P04896 · 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 0.83
- 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 0.68
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 P09681
- Every structure of UniProt P04896
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7DTY · PDBe 7DTY · UniProt P09681 · UniProt P04896 · UniProt P54311 · UniProt P63212
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