Research workbench
Orexin receptor 2 (OX2R) in complex with G protein and natural peptide-agonist orexin B (oxb)
Analyse Orexin receptor 2 (OX2R) in complex with G protein and natural peptide-agonist… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L1U
- Type
- protein
- Length
- 1,148 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, O43612
- Ligands
- NH2
- Pockets
- 10 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engineered guanine nucleotide-binding protein subunit alpha | protein | 228 | 44% 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 | 55% helix, 0% strand | P59768 |
| H | Single-chain antibody fv fragment (SVFV16) | protein | 233 | 3% helix, 45% strand | — |
| R | Hypocretin receptor type 2 | protein | 281 | 75% helix, 4% strand | Q548Y0 |
| L | Orexin | protein | 9 | 0% helix, 0% strand | O43612 |
Ligands and binding sites
- NH2 · Amino group · ion · chains R, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.81 | 0.85 | 56 | empty |
| 2 | 910 | 0.70 | 0.75 | 81 | empty |
| 3 | 383 | 0.67 | 0.80 | 54 | empty |
| 4 | 181 | 0.49 | 0.76 | 19 | empty |
| 5 | 170 | 0.49 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2155 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1299 Ų buried · 8 hydrogen bonds · protein-protein
- A–R · 1046 Ų buried · 8 hydrogen bonds · protein-protein
- R–L · 852 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 589 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7L1U · Orexin Receptor 2 (OX2R) in Complex with G Protein and Natural Peptide-Agonist Orexin B… · the same entry in another collection · chain L against L, 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 0.99
- 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 0.94
- O43612 · AlphaFold monomer V2.0 prediction for orexin (O43612) · a predicted model of the same protein · chain L against A, TM-score 0.37
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
- Every structure of UniProt O43612
- Elsewhere: RCSB PDB 7L1U · PDBe 7L1U · UniProt P62873 · UniProt P59768 · UniProt Q548Y0 · UniProt O43612
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.