Research workbench
Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin delineates the ligand binding specificity
Analyse Cryo-EM structure of human somatostatin receptor 2 complex with its agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WJ5
- Type
- protein
- Length
- 1,129 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P30874
- Pockets
- 12 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 214 | 41% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 6% helix, 48% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 49% helix, 0% strand | P59768 |
| E | GAI1 antibody (SCFV16) | protein | 232 | 4% helix, 46% strand | — |
| R | Soluble cytochrome B562,SOMATOSTATIN receptor type 2 | protein | 282 | 75% helix, 4% strand | P30874 |
| S | Somatostatin-14 (sst-14) | protein | 12 | 0% helix, 33% strand | — |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.82 | 0.85 | 64 | empty |
| 2 | 917 | 0.75 | 0.78 | 88 | empty |
| 3 | 108 | 0.59 | 0.86 | 24 | empty |
| 4 | 248 | 0.59 | 0.79 | 37 | empty |
| 5 | 212 | 0.57 | 0.80 | 43 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2011 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 1214 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1099 Ų buried · 9 hydrogen bonds · protein-protein
- R–S · 1071 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 587 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7WJ5 · Cryo-EM structure of human somatostatin receptor 2 complex with its agonist somatostatin… · the same entry in another collection · chain S against S, 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 C against A, TM-score 0.91
- P30874 · AlphaFold monomer V2.0 prediction for somatostatin receptor type 2 (P30874) · a predicted model of the same protein · chain R against A, TM-score 0.91
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P30874
- Elsewhere: RCSB PDB 7WJ5 · PDBe 7WJ5 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P30874
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