MolNFT v1 · #190584 · protein
Cryo-EM structure of the spexin-bound GALR2-minigq complex
7XJL: “Cryo-EM structure of the spexin-bound GALR2-minigq complex”. Electron microscopy, 12 pockets (best druggability 0.82). MolNFT v1 #190584 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XJL
- Type
- protein
- Length
- 1,137 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spexin; Guanine nucleotide-binding protein G(Q) subunit alpha; Guanine nucleotide-binding…
- UniProt
- P62873, P59768, O43603
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spexin | protein | 14 | 57% helix, 0% strand | — |
| B | Guanine nucleotide-binding protein G(Q) subunit alpha | protein | 226 | 47% helix, 18% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 45% strand | P62873 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 51 | 57% helix, 0% strand | P59768 |
| E | Single-chain variable fragment (SCFV16) | protein | 230 | 3% helix, 49% strand | — |
| F | Galanin receptor type 2 | protein | 278 | 81% helix, 4% strand | O43603 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.82 | 0.85 | 61 | empty |
| 2 | 112 | 0.77 | 0.96 | 28 | empty |
| 3 | 1136 | 0.76 | 0.78 | 96 | empty |
| 4 | 95 | 0.58 | 0.87 | 20 | empty |
| 5 | 132 | 0.54 | 0.81 | 29 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1917 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1145 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 1099 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 906 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 576 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7XJL · Cryo-EM structure of the spexin-bound GALR2-miniGq complex · the same entry in another collection · chain F against F, 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 C against A, TM-score 0.99
- O43603 · AlphaFold monomer V2.0 prediction for galanin receptor type 2 (O43603) · a predicted model of the same protein · chain F against A, TM-score 0.92
- 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 D against A, TM-score 0.91
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 O43603
- Elsewhere: RCSB PDB 7XJL · PDBe 7XJL · UniProt P62873 · UniProt P59768 · UniProt O43603
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