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Structure of the orexin-2 RECEPTOR(OX2R) bound to tak-925, gi and SCFV16

Analyse Structure of the orexin-2 RECEPTOR(OX2R) bound to tak-925, gi and SCFV16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7SQO
Type: protein
Length: 1,111 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Orexin receptor type 2; Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine…
UniProt: O43614, P63096, P62871, P63212
Ligands: OLA, A6F
Pockets: 12 · best druggability 0.82

Structure

electron microscopy · 5 distinct chains · 34% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Orexin receptor type 2	protein	270	79% helix, 1% strand	O43614
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	217	46% helix, 16% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 41% strand	P62871
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	54	63% helix, 0% strand	P63212
E	Scfv-16	protein	232	3% helix, 44% strand	—

Ligands and binding sites

OLA · Oleic acid · ligand · 4 copies · chains R
A6F · methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate · ligand · chains R

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	697	0.82	0.86	59	empty
2	549	0.81	0.86	42	A6F
3	788	0.67	0.74	69	empty
4	371	0.61	0.77	35	empty
5	166	0.52	0.79	31	empty

Interfaces

6 interfaces between chains.

B–G · 2223 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1243 Å² buried · 13 hydrogen bonds · protein-protein
R–A · 836 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 597 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 489 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7SQO · Structure of the orexin-2 receptor(OX2R) bound to TAK-925, Gi and scFv16 · the same entry in another collection · chain E against E, TM-score 1.00
P62871 · 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
O43614 · AlphaFold monomer V2.0 prediction for orexin receptor type 2 (O43614) · 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
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 0.71

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 O43614
Every structure of UniProt P63096
Every structure of UniProt P62871
Every structure of UniProt P63212
Elsewhere: RCSB PDB 7SQO · PDBe 7SQO · UniProt O43614 · UniProt P63096 · UniProt P62871 · UniProt P63212

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