MolNFT v2 · #213479 · protein
Cryo-EM structure of GIPR splice variant 2 (SV2) in complex with Gs protein
8ITM · Gastric inhibitory polypeptide receptor: “Cryo-EM structure of GIPR splice variant 2 (SV2) in complex with Gs protein”. Electron microscopy at 3.13, 11 pockets (best druggability 0.85). MolNFT v2 #213479 on GenesisL1: 3D structure…
- PDB
- 8ITM
- Type
- protein
- Length
- 1,035 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.13
- Source
- Bos taurus; Homo sapiens; Rattus norvegicus; synthetic construct
- Molecule
- Gastric inhibitory polypeptide receptor; Guanine nucleotide-binding protein G(s) subunit…
- UniProt
- P48546, P04896, P54311, P63212
- Pockets
- 11 · best druggability 0.85
Structure
electron microscopy · resolution 3.13 · 5 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Gastric inhibitory polypeptide receptor | protein | 278 | 81% helix, 0% strand | P48546 |
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 232 | 48% helix, 16% strand | P04896 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 341 | 9% helix, 45% 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 | 127 | 5% helix, 37% strand | — |
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.85 | 0.86 | 79 | empty |
| 2 | 337 | 0.72 | 0.84 | 49 | empty |
| 3 | 561 | 0.72 | 0.80 | 63 | empty |
| 4 | 800 | 0.71 | 0.77 | 63 | empty |
| 5 | 642 | 0.70 | 0.78 | 57 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2171 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1459 Ų buried · 15 hydrogen bonds · protein-protein
- R–A · 1028 Ų buried · 7 hydrogen bonds · protein-protein
- A–N · 888 Ų buried · 13 hydrogen bonds · protein-protein
- B–N · 462 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 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
- P48546 · AlphaFold monomer V2.0 prediction for gastric inhibitory polypeptide receptor (P48546) · a predicted model of the same protein · chain R against A, TM-score 0.87
- 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 0.67
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 P48546
- Every structure of UniProt P04896
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 8ITM · PDBe 8ITM · UniProt P48546 · UniProt P04896 · UniProt P54311 · UniProt P63212
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