7L1V: Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1

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PDB ID: 7L1VDownload
MMDB ID: 198673
PDB Deposition Date: 2020/12/15
Updated in MMDB: 2024/11
Experimental Method:
electron microscopy
Resolution: 3  Å
Source Organism:
Mus musculus
Similar Structures:
Biological Unit for 7L1V: hexameric; determined by author
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7L1V: Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1
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AA: Engineered Guanine nucleotide-binding protein subunit alphaBB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1CC: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2HH: single-chain antibody Fv fragment (svFv16)RR: Hypocretin receptor type 2SS: Synthetic nanobody 51 (Sb51)1XGD: 4'-methoxy-N,N-dimethyl-3'-{[3-(2-{[2-(2H-1,2,3-triazol-2-yl)benzene-1-carbonyl]amino}ethyl)phenyl]sulfamoyl}[1,1'-biphenyl]-3-carboxamide
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Molecular Components in 7L1V
Label Count Molecule
Proteins (6 molecules)
1
Engineered Guanine Nucleotide-binding Protein Subunit Alpha
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
175150225244244 residues, click to see VAST similar structures.helix 5-30helix 43-50helix 116-128helix 144-153helix 182-199helix 221-240strand 31-38strand 68-75strand 76-83strand 102-110strand 136-143strand 208-215Domain 1 (31-244): click to see VAST similar structures1adenylyl cyclase interaction siteadenylyl cyclase interaction site(5)location: 67, residue: Ilocation: 92, residue: Rlocation: 95, residue: Ilocation: 96, residue: Qlocation: 99, residue: Nbeta - gamma complex interaction sitebeta - gamma complex interaction site(14)location: 67, residue: Ilocation: 69, residue: Elocation: 80, residue: Hlocation: 82, residue: Flocation: 86, residue: Glocation: 87, residue: Qlocation: 88, residue: Rlocation: 90, residue: Elocation: 93, residue: Klocation: 94, residue: Wlocation: 96, residue: Qlocation: 97, residue: Clocation: 98, residue: Flocation: 99, residue: Nputative receptor binding siteputative receptor binding site(16)location: 207, residue: Hlocation: 208, residue: Ilocation: 209, residue: Clocation: 210, residue: Ylocation: 211, residue: Plocation: 212, residue: Hlocation: 213, residue: Flocation: 214, residue: Tlocation: 215, residue: Clocation: 216, residue: Alocation: 217, residue: Vlocation: 218, residue: Dlocation: 220, residue: Elocation: 221, residue: Nlocation: 222, residue: Alocation: 223, residue: RSwitch II regionSwitch II region(17)location: 84, residue: Vlocation: 85, residue: Glocation: 86, residue: Glocation: 87, residue: Qlocation: 88, residue: Rlocation: 89, residue: Dlocation: 90, residue: Elocation: 91, residue: Rlocation: 92, residue: Rlocation: 93, residue: Klocation: 94, residue: Wlocation: 95, residue: Ilocation: 96, residue: Qlocation: 97, residue: Clocation: 98, residue: Flocation: 99, residue: Nlocation: 100, residue: DG3 boxG3 box(4)location: 83, residue: Dlocation: 84, residue: Vlocation: 85, residue: Glocation: 86, residue: GG4 boxG4 box(4)location: 142, residue: Nlocation: 143, residue: Klocation: 144, residue: Qlocation: 145, residue: DG5 boxG5 box(3)location: 215, residue: Clocation: 216, residue: Alocation: 217, residue: VG-alphacd00066 (67-238): Alpha subunit of G proteins (guanine nucleotide binding)P-loop_NTPase superfamilycl38936(67-238): Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A...
1
Guanine Nucleotide-binding Protein G(i)/g(s)/g(t) Subunit Beta-1
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
175150225300349349 residues, click to see VAST similar structures.helix 14-34strand 55-61strand 65-73strand 77-85strand 86-94strand 95-104strand 108-115strand 119-126strand 129-135strand 145-149strand 153-162strand 164-172strand 173-181strand 182-190strand 194-202strand 206-214strand 215-223strand 224-232strand 236-244strand 248-256strand 257-265strand 266-274strand 281-288strand 292-299strand 301-308strand 311-318strand 322-330strand 335-342strand 343-349Domain 1 (45-192): click to see VAST similar structures1Domain 2 (193-320): click to see VAST similar structures2Domain 1 (321-349): click to see VAST similar structures1structural tetrad(40)location: 63, residue: Hlocation: 81, residue: Slocation: 85, residue: Dlocation: 91, residue: Wlocation: 92, residue: Dlocation: 99, residue: Vlocation: 100, residue: Hlocation: 123, residue: Clocation: 127, residue: Dlocation: 133, residue: Ylocation: 134, residue: Nlocation: 150, residue: Glocation: 151, residue: Hlocation: 168, residue: Tlocation: 172, residue: Dlocation: 178, residue: Wlocation: 179, residue: Dlocation: 192, residue: Hlocation: 209, residue: Vlocation: 214, residue: Dlocation: 220, residue: Wlocation: 221, residue: Dlocation: 233, residue: Glocation: 234, residue: Hlocation: 252, residue: Tlocation: 256, residue: Dlocation: 262, residue: Flocation: 263, residue: Dlocation: 274, residue: Slocation: 275, residue: Hlocation: 295, residue: Llocation: 300, residue: Dlocation: 306, residue: Wlocation: 307, residue: Dlocation: 319, residue: Glocation: 320, residue: Hlocation: 338, residue: Tlocation: 342, residue: Dlocation: 348, residue: Wlocation: 349, residue: NWD40cd00200 (57-349): WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assemblyWD40 superfamilycl29593(57-349): WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal...
1
Guanine Nucleotide-binding Protein G(i)/g(s)/g(o) Subunit Gamma-2
1 Protein
SS Diagram
Features
Domain Families
Specific Hits
Super Families
1507171 residues, click to see VAST similar structures.helix 8-23helix 30-44beta subunit binding sitebeta subunit binding site(15)location: 9, residue: Ilocation: 12, residue: Alocation: 16, residue: Vlocation: 19, residue: Llocation: 23, residue: Alocation: 28, residue: Ilocation: 30, residue: Vlocation: 33, residue: Alocation: 34, residue: Alocation: 37, residue: Llocation: 38, residue: Mlocation: 41, residue: Clocation: 50, residue: Llocation: 51, residue: Llocation: 61, residue: FGGLsmart00224 (9-71): G protein gamma subunit-like motifsGGLcl00069(9-71): G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G...
1
Single-chain Antibody FV Fragment (Svfv16)
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
175150225250250 residues, click to see VAST similar structures.strand 4-10strand 11-15strand 16-28strand 34-42strand 47-55strand 59-63strand 69-76strand 79-89strand 93-102strand 112-121strand 140-144strand 147-151strand 153-165strand 167-170strand 172-182strand 187-193strand 195-198strand 204-211strand 212-222strand 226-234strand 239-242strand 244-248Domain 1 (1-130): click to see VAST similar structures1Domain 2 (131-250): click to see VAST similar structures2heterodimer interfaceheterodimer interface(6)location: 41, residue: Qlocation: 45, residue: Klocation: 49, residue: Wlocation: 97, residue: Ylocation: 113, residue: Wlocation: 114, residue: Gantigen binding siteantigen binding site(3)location: 35, residue: Glocation: 52, residue: Ylocation: 101, residue: Sintrachain IgC domain interfaceintrachain IgC domain interface(4)location: 11, residue: Glocation: 13, residue: Llocation: 118, residue: Tlocation: 120, residue: Theterodimer interfaceheterodimer interface(7)location: 177, residue: Ylocation: 179, residue: Flocation: 181, residue: Qlocation: 186, residue: Slocation: 189, residue: Llocation: 193, residue: Rlocation: 230, residue: Yantigen binding siteantigen binding site(5)location: 174, residue: Tlocation: 175, residue: Ylocation: 192, residue: Ylocation: 196, residue: Nlocation: 235, residue: Lintrachain IgC domain interfaceintrachain IgC domain(4)location: 150, residue: Plocation: 246, residue: Klocation: 248, residue: Elocation: 249, residue: LIgV_Hcd04981 (5-121): Immunoglobulin (Ig) heavy chain (H), variable (V) domainIg superfamilycl11960(5-121): The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins,...IgV_L_kappacd04980 (140-249): Immunoglobulin (Ig) light chain, kappa type, variable (V) domainIg superfamilycl11960(140-249): The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins,...
1
Hypocretin Receptor Type 2
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
175150225300374374 residues, click to see VAST similar structures.helix 64-87helix 97-123helix 130-162helix 172-189helix 225-253helix 270-303helix 315-334helix 344-351strand 196-203strand 212-219Domain 1 (1-339): click to see VAST similar structures1putative peptide ligand binding pocketputative peptide(41)location: 117, residue: Tlocation: 120, residue: Vlocation: 121, residue: Dlocation: 133, residue: Clocation: 134, residue: Klocation: 135, residue: Vlocation: 136, residue: Ilocation: 137, residue: Plocation: 138, residue: Ylocation: 140, residue: Qlocation: 141, residue: Tlocation: 144, residue: Vlocation: 187, residue: Clocation: 189, residue: Ilocation: 190, residue: Mlocation: 191, residue: Ilocation: 192, residue: Plocation: 193, residue: Qlocation: 226, residue: Plocation: 229, residue: Ylocation: 230, residue: Hlocation: 231, residue: Ilocation: 233, residue: Flocation: 234, residue: Flocation: 235, residue: Llocation: 237, residue: Tlocation: 238, residue: Ylocation: 292, residue: Ylocation: 295, residue: Ilocation: 296, residue: Slocation: 298, residue: Llocation: 299, residue: Nlocation: 302, residue: Klocation: 317, residue: Vlocation: 318, residue: Ylocation: 320, residue: Wlocation: 321, residue: Flocation: 322, residue: Tlocation: 325, residue: Hlocation: 328, residue: Vlocation: 329, residue: Y7tmA_OXRcd15208 (61-350): orexin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors7tm_GPCRs superfamilycl28897(61-350): This hierarchical evolutionary model represents the seven-transmembrane (7TM) receptors, often referred to as G protein-coupled receptors (GPCRs),...
1
Synthetic Nanobody 51 (Sb51)
1 Protein
SS Diagram
Domain Families
Super Families
175118118 residues, click to see VAST similar structures.strand 8-12strand 13-16strand 18-30strand 35-43strand 48-56strand 60-64strand 70-78strand 79-90strand 94-103strand 105-109strand 111-115Ig superfamilycl11960(7-117): Chain S, Synthetic nanobody 51 (Sb51)
Chemical and Non-standard biopolymers (1 molecule)
1
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