Research workbench
Xfel crystal structure of human melatonin receptor MT1 in complex with agomelatine
Analyse Xfel crystal structure of human melatonin receptor MT1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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