Research workbench
Crystal structure of the orexin-2 receptor in complex with empa at 2.74 a resolution
Analyse Crystal structure of the orexin-2 receptor in complex with empa at 2.74 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TPG
- Type
- protein
- Length
- 504 residues
- Chains
- 1
- 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
- 7MA, OLA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Orexin receptor type 2,GLGA glycogen SYNTHASE,HYPOCRETIN receptor-2 | protein | 504 | 66% helix, 8% strand | O43614, Q9V2J8, Q548Y0 |
Ligands and binding sites
- 7MA · N-ethyl-2-[(6-methoxypyridin-3-yl)-(2-methylphenyl) sulfonyl-amino]-N-(pyridin-3-ylmethyl)ethanamide · ligand · chains A
- OLA · Oleic acid · ligand · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.82 | 0.85 | 60 | 7MA, PG4 |
| 2 | 174 | 0.49 | 0.77 | 25 | empty |
| 3 | 191 | 0.47 | 0.75 | 29 | empty |
| 4 | 76 | 0.34 | 0.75 | 12 | empty |
| 5 | 71 | 0.33 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, alkylation).
Compared structures
- 6TPG · Crystal structure of the Orexin-2 receptor in complex with EMPA at 2.74 A resolution · the same entry in another collection · chain A against A, 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 0.64
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 6TPG · PDBe 6TPG · UniProt O43614 · UniProt Q9V2J8 · UniProt Q548Y0
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