MolNFT v1 · #156747 · protein
Xfel crystal structure of human melatonin receptor MT1 in complex with agomelatine
6ME5 · Chimera protein of melatonin receptor type 1A and glga…: “Xfel crystal structure of human melatonin receptor MT1 in complex with agomelatine”. X-ray diffraction, 2 ligands (AWY, OLA), 6 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6ME5
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera protein of melatonin receptor type 1A and glga glycogen synthase
- UniProt
- P48039, Q9V2J8
- Ligands
- AWY, OLA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera protein of melatonin receptor type 1A and glga glycogen synthase | protein | 485 | 68% helix, 8% strand | P48039, Q9V2J8 |
Ligands and binding sites
- AWY · ~{N}-[2-(7-methoxynaphthalen-1-yl)ethyl]ethanamide · ligand · chains A
- OLA · Oleic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.81 | 0.93 | 34 | AWY |
| 2 | 180 | 0.50 | 0.77 | 30 | empty |
| 3 | 55 | 0.46 | 0.84 | 18 | empty |
| 4 | 91 | 0.40 | 0.77 | 27 | empty |
| 5 | 85 | 0.40 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, alkylation).
Compared structures
- 6ME5 · XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine · the same entry in another collection · chain A against A, TM-score 1.00
- P48039 · AlphaFold monomer V2.0 prediction for melatonin receptor type 1A (P48039) · a predicted model of the same protein · chain A against A, TM-score 0.59
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 P48039
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 6ME5 · PDBe 6ME5 · UniProt P48039 · UniProt Q9V2J8
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