Research workbench
XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon
Analyse XFEL crystal structure of human melatonin receptor MT2 in complex with ramelteon in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ME9
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Clostridium pasteurianum; Escherichia coli; Homo sapiens
- Molecule
- Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin
- UniProt
- P0ABE7, P49286, P00268
- Ligands
- JEV, ZN
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.3 · 2 distinct chains · 71% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin | protein | 448 | 67% helix, 4% strand | P0ABE7, P49286, P00268 |
| B | Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin | protein | 395 | 77% helix, 2% strand | P0ABE7, P49286, P00268 |
Ligands and binding sites
- JEV · N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.84 | 0.96 | 37 | JEV |
| 2 | 265 | 0.83 | 0.94 | 44 | JEV |
| 3 | 1109 | 0.77 | 0.79 | 108 | empty |
| 4 | 810 | 0.72 | 0.77 | 91 | empty |
| 5 | 463 | 0.58 | 0.74 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 742 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ME9 · Xfel crystal structure of human melatonin receptor MT2 in complex with ramelteon · the same entry in another collection · chain A against A, TM-score 1.00
- P49286 · AlphaFold monomer V2.0 prediction for melatonin receptor type 1B (P49286) · a predicted model of the same protein · chain B against A, TM-score 0.71
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.26
- P00268 · AlphaFold monomer V2.0 prediction for rubredoxin (P00268) · a predicted model of the same protein · chain A against A, TM-score 0.12
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 P0ABE7
- Every structure of UniProt P49286
- Every structure of UniProt P00268
- Elsewhere: RCSB PDB 6ME9 · PDBe 6ME9 · UniProt P0ABE7 · UniProt P49286 · UniProt P00268
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