MolNFT v1 · #165269 · protein
Crystal structure of the orexin-2 receptor in complex with suvorexant at 2.76 a resolution
6TPJ · Orexin receptor type 2,GLGA glycogen SYNTHASE,HYPOCRETIN…: “Crystal structure of the orexin-2 receptor in complex with suvorexant at 2.76 a resolution”. X-ray diffraction, 3 ligands (OLA, SUV, NH4), 13 pockets (best druggability…
- PDB
- 6TPJ
- Type
- protein
- Length
- 1,000 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Orexin receptor type 2,GLGA glycogen SYNTHASE,HYPOCRETIN receptor-2
- UniProt
- O43614, Q9V2J8, Q548Y0
- Ligands
- OLA, SUV, NH4
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orexin receptor type 2,GLGA glycogen SYNTHASE,HYPOCRETIN receptor-2 | protein | 499 | 66% helix, 8% strand | O43614, Q9V2J8, Q548Y0 |
| B | Orexin receptor type 2,GLGA glycogen SYNTHASE,HYPOCRETIN receptor-2 | protein | 501 | 65% helix, 8% strand | O43614, Q9V2J8, Q548Y0 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 34 copies · chains A, B
- SUV · [(7R)-4-(5-chloro-1,3-benzoxazol-2-yl)-7-methyl-1,4-diazepan-1-yl][5-methyl-2-(2H-1,2,3-triazol-2-yl) phenyl]methanone · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 5 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.83 | 0.87 | 58 | SUV, PG4 |
| 2 | 645 | 0.83 | 0.87 | 53 | SUV, PG4 |
| 3 | 628 | 0.73 | 0.80 | 70 | OLA |
| 4 | 183 | 0.52 | 0.77 | 18 | OLA |
| 5 | 200 | 0.49 | 0.75 | 31 | NH4, OLA |
Interfaces
1 interface between chains.
- A–B · 560 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, alkylation).
Compared structures
- 6TPJ · Crystal structure of the Orexin-2 receptor in complex with suvorexant at 2.76 A resolution · the same entry in another collection · chain B against B, TM-score 1.00
- O43614 · AlphaFold monomer V2.0 prediction for orexin receptor type 2 (O43614) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 Q9V2J8
- Every structure of UniProt Q548Y0
- Elsewhere: RCSB PDB 6TPJ · PDBe 6TPJ · UniProt O43614 · UniProt Q9V2J8 · UniProt Q548Y0
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