MolNFT v1 · #156750 · protein
Xfel crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin
6ME8 · Soluble cytochrome B562,MELATONIN receptor type 1B…: “Xfel crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin”. X-ray diffraction, 2 ligands (JEY, ZN), 9 pockets (best druggability 0.83).…
- PDB
- 6ME8
- Type
- protein
- Length
- 843 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,MELATONIN receptor type 1B, rubredoxin
- UniProt
- P0ABE7, P49286, P00268
- Ligands
- JEY, ZN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble cytochrome B562,MELATONIN receptor type 1B, rubredoxin | protein | 449 | 69% helix, 4% strand | P0ABE7, P49286, P00268 |
| B | Soluble cytochrome B562,MELATONIN receptor type 1B, rubredoxin | protein | 394 | 78% helix, 2% strand | P0ABE7, P49286, P00268 |
Ligands and binding sites
- JEY · N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.83 | 0.96 | 36 | JEY |
| 2 | 956 | 0.80 | 0.82 | 120 | JEY |
| 3 | 1121 | 0.77 | 0.79 | 104 | empty |
| 4 | 225 | 0.61 | 0.81 | 24 | empty |
| 5 | 60 | 0.52 | 0.86 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6ME8 · XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with… · 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 0.72
- 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 6ME8 · PDBe 6ME8 · UniProt P0ABE7 · UniProt P49286 · UniProt P00268
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