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Cryo-EM structure of the L-054,264-bound human SSTR2-GI1 complex

Analyse Cryo-EM structure of the L-054,264-bound human SSTR2-GI1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WIG
Type: protein
Length: 1,139 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Somatostatin receptor type 2; Guanine nucleotide-binding protein G(I) subunit alpha-1…
UniProt: P30874, P63096, P54311, P63212
Ligands: 9FI
Pockets: 10 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Somatostatin receptor type 2	protein	283	80% helix, 2% strand	P30874
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	225	43% helix, 18% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 47% strand	P54311
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	58	55% helix, 0% strand	P63212
S	Single Fab chain (SVFV16)	protein	234	4% helix, 47% strand	—

Ligands and binding sites

9FI · ~{N}-[(2~{R})-1-[[(1~{R},3~{S})-3-(aminomethyl) cyclohexyl]methylamino]-3-(1~{H}-indol-3-yl)-1-oxidanylidene-propan-2-yl]spiro[indene-1,4'-piperidine]-1'-carboxamide · ligand · chains R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	844	0.83	0.85	70	empty
2	842	0.77	0.80	60	9FI
3	865	0.70	0.76	80	empty
4	246	0.55	0.77	29	empty
5	230	0.54	0.78	30	empty

Interfaces

5 interfaces between chains.

B–G · 2231 Å² buried · 16 hydrogen bonds · protein-protein
R–A · 1220 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 1166 Å² buried · 16 hydrogen bonds · protein-protein
A–S · 567 Å² buried · 9 hydrogen bonds · protein-protein
B–S · 433 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7WIG · Cryo-EM structure of the L-054,264-bound human SSTR2-Gi1 complex · the same entry in another collection · chain S against S, 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
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 0.90
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 0.83
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 0.66

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 P30874
Every structure of UniProt P63096
Every structure of UniProt P54311
Every structure of UniProt P63212
Elsewhere: RCSB PDB 7WIG · PDBe 7WIG · UniProt P30874 · UniProt P63096 · UniProt P54311 · UniProt P63212

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