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7L1V:
Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1
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PDB ID:
7L1V
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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
▼
Taxonomy
Molecule
Mus musculus
H
Lama glama
S
Homo sapiens
A, B, C, R
Similar Structures:
VAST+
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Biological Unit
Asymmetric Unit
Biological Unit for 7L1V: hexameric; determined by author
Molecular Graphic
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Interactions
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A
A: Engineered Guanine nucleotide-binding protein subunit alpha
B
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
C
C: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H
H: single-chain antibody Fv fragment (svFv16)
R
R: Hypocretin receptor type 2
S
S: Synthetic nanobody 51 (Sb51)
1
XGD: 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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Protein
Nucleotide
Chemical
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Format:
ASN.1 (Cn3D)
PDB
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PNG (image)
Data Set:
alpha-Carbons
Single 3D structure
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Molecular Components in 7L1V
Label
Count
Molecule
Proteins (6 molecules)
A
1
Engineered Guanine Nucleotide-binding Protein Subunit Alpha
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
75
150
225
244
244 residues, click to see VAST similar structures.
helix 5-30
helix 43-50
helix 116-128
helix 144-153
helix 182-199
helix 221-240
strand 31-38
strand 68-75
strand 76-83
strand 102-110
strand 136-143
strand 208-215
Domain 1 (31-244): click to see VAST similar structures
1
adenylyl cyclase interaction site
adenylyl cyclase interaction site(5)
location: 67, residue: I
location: 92, residue: R
location: 95, residue: I
location: 96, residue: Q
location: 99, residue: N
beta - gamma complex interaction site
beta - gamma complex interaction site(14)
location: 67, residue: I
location: 69, residue: E
location: 80, residue: H
location: 82, residue: F
location: 86, residue: G
location: 87, residue: Q
location: 88, residue: R
location: 90, residue: E
location: 93, residue: K
location: 94, residue: W
location: 96, residue: Q
location: 97, residue: C
location: 98, residue: F
location: 99, residue: N
putative receptor binding site
putative receptor binding site(16)
location: 207, residue: H
location: 208, residue: I
location: 209, residue: C
location: 210, residue: Y
location: 211, residue: P
location: 212, residue: H
location: 213, residue: F
location: 214, residue: T
location: 215, residue: C
location: 216, residue: A
location: 217, residue: V
location: 218, residue: D
location: 220, residue: E
location: 221, residue: N
location: 222, residue: A
location: 223, residue: R
Switch II region
Switch II region(17)
location: 84, residue: V
location: 85, residue: G
location: 86, residue: G
location: 87, residue: Q
location: 88, residue: R
location: 89, residue: D
location: 90, residue: E
location: 91, residue: R
location: 92, residue: R
location: 93, residue: K
location: 94, residue: W
location: 95, residue: I
location: 96, residue: Q
location: 97, residue: C
location: 98, residue: F
location: 99, residue: N
location: 100, residue: D
G3 box
G3 box(4)
location: 83, residue: D
location: 84, residue: V
location: 85, residue: G
location: 86, residue: G
G4 box
G4 box(4)
location: 142, residue: N
location: 143, residue: K
location: 144, residue: Q
location: 145, residue: D
G5 box
G5 box(3)
location: 215, residue: C
location: 216, residue: A
location: 217, residue: V
G-alpha
cd00066 (67-238): Alpha subunit of G proteins (guanine nucleotide binding)
P-loop_NTPase superfamily
cl38936(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...
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B
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
1
75
150
225
300
349
349 residues, click to see VAST similar structures.
helix 14-34
strand 55-61
strand 65-73
strand 77-85
strand 86-94
strand 95-104
strand 108-115
strand 119-126
strand 129-135
strand 145-149
strand 153-162
strand 164-172
strand 173-181
strand 182-190
strand 194-202
strand 206-214
strand 215-223
strand 224-232
strand 236-244
strand 248-256
strand 257-265
strand 266-274
strand 281-288
strand 292-299
strand 301-308
strand 311-318
strand 322-330
strand 335-342
strand 343-349
Domain 1 (45-192): click to see VAST similar structures
1
Domain 2 (193-320): click to see VAST similar structures
2
Domain 1 (321-349): click to see VAST similar structures
1
structural tetrad
(40)
location: 63, residue: H
location: 81, residue: S
location: 85, residue: D
location: 91, residue: W
location: 92, residue: D
location: 99, residue: V
location: 100, residue: H
location: 123, residue: C
location: 127, residue: D
location: 133, residue: Y
location: 134, residue: N
location: 150, residue: G
location: 151, residue: H
location: 168, residue: T
location: 172, residue: D
location: 178, residue: W
location: 179, residue: D
location: 192, residue: H
location: 209, residue: V
location: 214, residue: D
location: 220, residue: W
location: 221, residue: D
location: 233, residue: G
location: 234, residue: H
location: 252, residue: T
location: 256, residue: D
location: 262, residue: F
location: 263, residue: D
location: 274, residue: S
location: 275, residue: H
location: 295, residue: L
location: 300, residue: D
location: 306, residue: W
location: 307, residue: D
location: 319, residue: G
location: 320, residue: H
location: 338, residue: T
location: 342, residue: D
location: 348, residue: W
location: 349, residue: N
WD40
cd00200 (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 assembly
WD40 superfamily
cl29593(57-349): WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal...
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C
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
1
50
71
71 residues, click to see VAST similar structures.
helix 8-23
helix 30-44
beta subunit binding site
beta subunit binding site(15)
location: 9, residue: I
location: 12, residue: A
location: 16, residue: V
location: 19, residue: L
location: 23, residue: A
location: 28, residue: I
location: 30, residue: V
location: 33, residue: A
location: 34, residue: A
location: 37, residue: L
location: 38, residue: M
location: 41, residue: C
location: 50, residue: L
location: 51, residue: L
location: 61, residue: F
GGL
smart00224 (9-71): G protein gamma subunit-like motifs
GGL
cl00069(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...
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H
1
Single-chain Antibody FV Fragment (Svfv16)
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
75
150
225
250
250 residues, click to see VAST similar structures.
strand 4-10
strand 11-15
strand 16-28
strand 34-42
strand 47-55
strand 59-63
strand 69-76
strand 79-89
strand 93-102
strand 112-121
strand 140-144
strand 147-151
strand 153-165
strand 167-170
strand 172-182
strand 187-193
strand 195-198
strand 204-211
strand 212-222
strand 226-234
strand 239-242
strand 244-248
Domain 1 (1-130): click to see VAST similar structures
1
Domain 2 (131-250): click to see VAST similar structures
2
heterodimer interface
heterodimer interface(6)
location: 41, residue: Q
location: 45, residue: K
location: 49, residue: W
location: 97, residue: Y
location: 113, residue: W
location: 114, residue: G
antigen binding site
antigen binding site(3)
location: 35, residue: G
location: 52, residue: Y
location: 101, residue: S
intrachain IgC domain interface
intrachain IgC domain interface(4)
location: 11, residue: G
location: 13, residue: L
location: 118, residue: T
location: 120, residue: T
heterodimer interface
heterodimer interface(7)
location: 177, residue: Y
location: 179, residue: F
location: 181, residue: Q
location: 186, residue: S
location: 189, residue: L
location: 193, residue: R
location: 230, residue: Y
antigen binding site
antigen binding site(5)
location: 174, residue: T
location: 175, residue: Y
location: 192, residue: Y
location: 196, residue: N
location: 235, residue: L
intrachain IgC domain interface
intrachain IgC domain(4)
location: 150, residue: P
location: 246, residue: K
location: 248, residue: E
location: 249, residue: L
IgV_H
cd04981 (5-121): Immunoglobulin (Ig) heavy chain (H), variable (V) domain
Ig superfamily
cl11960(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_kappa
cd04980 (140-249): Immunoglobulin (Ig) light chain, kappa type, variable (V) domain
Ig superfamily
cl11960(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,...
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R
1
Hypocretin Receptor Type 2
1 Protein
SS Diagram
3D Domains
Features
Domain Families
Specific Hits
Super Families
1
75
150
225
300
374
374 residues, click to see VAST similar structures.
helix 64-87
helix 97-123
helix 130-162
helix 172-189
helix 225-253
helix 270-303
helix 315-334
helix 344-351
strand 196-203
strand 212-219
Domain 1 (1-339): click to see VAST similar structures
1
putative peptide ligand binding pocket
putative peptide(41)
location: 117, residue: T
location: 120, residue: V
location: 121, residue: D
location: 133, residue: C
location: 134, residue: K
location: 135, residue: V
location: 136, residue: I
location: 137, residue: P
location: 138, residue: Y
location: 140, residue: Q
location: 141, residue: T
location: 144, residue: V
location: 187, residue: C
location: 189, residue: I
location: 190, residue: M
location: 191, residue: I
location: 192, residue: P
location: 193, residue: Q
location: 226, residue: P
location: 229, residue: Y
location: 230, residue: H
location: 231, residue: I
location: 233, residue: F
location: 234, residue: F
location: 235, residue: L
location: 237, residue: T
location: 238, residue: Y
location: 292, residue: Y
location: 295, residue: I
location: 296, residue: S
location: 298, residue: L
location: 299, residue: N
location: 302, residue: K
location: 317, residue: V
location: 318, residue: Y
location: 320, residue: W
location: 321, residue: F
location: 322, residue: T
location: 325, residue: H
location: 328, residue: V
location: 329, residue: Y
7tmA_OXR
cd15208 (61-350): orexin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors
7tm_GPCRs superfamily
cl28897(61-350): This hierarchical evolutionary model represents the seven-transmembrane (7TM) receptors, often referred to as G protein-coupled receptors (GPCRs),...
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S
1
Synthetic Nanobody 51 (Sb51)
1 Protein
SS Diagram
Domain Families
Super Families
1
75
118
118 residues, click to see VAST similar structures.
strand 8-12
strand 13-16
strand 18-30
strand 35-43
strand 48-56
strand 60-64
strand 70-78
strand 79-90
strand 94-103
strand 105-109
strand 111-115
Ig superfamily
cl11960(7-117): Chain S, Synthetic nanobody 51 (Sb51)
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Chemical and Non-standard biopolymers (1 molecule)
1
1
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
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH.
"
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Nucleic Acids Res. 2014 Jan; 42(Database issue)
:D297-303
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