Research workbench
Orexin receptor 2 (OX2R) in complex with G protein and small-molecule agonist compound 1
Analyse Orexin receptor 2 (OX2R) in complex with G protein and small-molecule agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L1V
- Type
- protein
- Length
- 1,253 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered guanine nucleotide-binding protein subunit alpha; Guanine nucleotide-binding…
- UniProt
- P62873, P59768, Q548Y0
- Ligands
- XGD
- Pockets
- 10 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engineered guanine nucleotide-binding protein subunit alpha | protein | 228 | 42% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 46% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 59% helix, 0% strand | P59768 |
| H | Single-chain antibody fv fragment (SVFV16) | protein | 233 | 1% helix, 46% strand | — |
| R | Hypocretin receptor type 2 | protein | 284 | 73% helix, 5% strand | Q548Y0 |
| S | Synthetic nanobody 51 (SB51) | protein | 111 | 3% helix, 53% strand | — |
Ligands and binding sites
- 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 · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.87 | 0.88 | 62 | XGD |
| 2 | 767 | 0.83 | 0.86 | 57 | empty |
| 3 | 701 | 0.67 | 0.75 | 61 | empty |
| 4 | 382 | 0.66 | 0.80 | 59 | empty |
| 5 | 207 | 0.57 | 0.79 | 28 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2211 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1245 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 1074 Ų buried · 6 hydrogen bonds · protein-protein
- R–S · 1050 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 582 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7L1V · Orexin Receptor 2 (OX2R) in Complex with G Protein and Small-Molecule Agonist Compound 1 · the same entry in another collection · chain S against S, TM-score 1.00
- P62873 · 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 1.00
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q548Y0
- Elsewhere: RCSB PDB 7L1V · PDBe 7L1V · UniProt P62873 · UniProt P59768 · UniProt Q548Y0
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