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Cryo-EM structure of human GPR158

Analyse Cryo-EM structure of human GPR158 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SHE
Type: protein
Length: 1,081 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: G-protein coupled receptor 158
UniProt: Q5T848
Ligands: CLR, PEE, EIJ
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 2 distinct chains · 39% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	G-protein coupled receptor 158	protein	541	41% helix, 7% strand	Q5T848
B	G-protein coupled receptor 158	protein	540	38% helix, 4% strand	Q5T848

Ligands and binding sites

CLR · Cholesterol · ligand · 22 copies · chains A, B
PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · chains A, B
EIJ · (2S)-1-{[(S)-hydroxy{[(1s,2r,3r,4r,5s,6s)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5E,8E,11E,14E)-icosa-5, 8,11,14-tetraenoate · ligand · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.80	0.90	56	empty
2	877	0.80	0.82	50	PEE, EIJ
3	270	0.79	0.91	52	empty
4	465	0.75	0.84	56	empty
5	332	0.72	0.84	42	empty

Interfaces

1 interface between chains.

A–B · 2229 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

7SHE · Cryo-EM structure of human GPR158 · the same entry in another collection · chain A against A, TM-score 1.00
Q5T848 · AlphaFold monomer V2.0 prediction for probable G-protein coupled receptor 158 (Q5T848) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 Q5T848
Elsewhere: RCSB PDB 7SHE · PDBe 7SHE · UniProt Q5T848

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