Research workbench
Cryo-EM structure of a class a orphan GPCR
Analyse Cryo-EM structure of a class a orphan GPCR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VUI
- Type
- protein
- Length
- 1,034 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short…
- EC
- 3.2.1.8
- UniProt
- P62873, P59768, Q6DWJ6
- Ligands
- GTP, 7ZQ, MG
- Pockets
- 14 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 234 | 47% helix, 16% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 42% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 54% helix, 0% strand | P59768 |
| N | Nanobody 35 | protein | 126 | 0% helix, 40% strand | — |
| R | Chimera of endo-1,4-beta-xylanase and probable G-protein coupled receptor 139 (EC 3.2.1.8) | protein | 279 | 80% helix, 0% strand | Q6DWJ6 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- 7ZQ · 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide · ligand · chains R
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.80 | 0.85 | 58 | empty |
| 2 | 1054 | 0.80 | 0.81 | 77 | empty |
| 3 | 556 | 0.76 | 0.83 | 49 | 7ZQ |
| 4 | 824 | 0.75 | 0.79 | 68 | empty |
| 5 | 485 | 0.72 | 0.82 | 60 | MG |
Interfaces
6 interfaces between chains.
- B–G · 1980 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1463 Ų buried · 20 hydrogen bonds · protein-protein
- A–R · 1247 Ų buried · 12 hydrogen bonds · protein-protein
- A–N · 903 Ų buried · 12 hydrogen bonds · protein-protein
- B–N · 592 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7VUI · Cryo-EM structure of a class A orphan GPCR · the same entry in another collection · chain R against R, 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 0.94
- Q6DWJ6 · AlphaFold monomer V2.0 prediction for probable G-protein coupled receptor 139 (Q6DWJ6) · a predicted model of the same protein · chain R against A, TM-score 0.88
- P09850 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P09850) · a predicted model of the same protein · chain R against A, TM-score 0.19
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q6DWJ6
- Elsewhere: RCSB PDB 7VUI · PDBe 7VUI · UniProt P62873 · UniProt P59768 · UniProt Q6DWJ6
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