Research workbench
Human melatonin receptor MT1 - GI1 complex
Analyse Human melatonin receptor MT1 - GI1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DB6
- Type
- protein
- Length
- 1,116 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P63212, P48039
- Ligands
- JEV
- Pockets
- 12 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 219 | 34% helix, 15% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 47% strand | — |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 36% helix, 0% strand | P63212 |
| E | SCFV16 | protein | 232 | 3% helix, 47% strand | — |
| D | Melatonin receptor type 1A | protein | 276 | 70% helix, 1% strand | P48039 |
Ligands and binding sites
- JEV · N-{2-[(8S)-1,6,7,8-tetrahydro-2H-indeno[5,4-b]furan-8-yl]ethyl}propanamide · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.81 | 0.92 | 47 | JEV |
| 2 | 715 | 0.81 | 0.85 | 67 | empty |
| 3 | 307 | 0.79 | 0.89 | 54 | empty |
| 4 | 1168 | 0.76 | 0.78 | 87 | empty |
| 5 | 93 | 0.51 | 0.83 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1989 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1300 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1164 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 623 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 482 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7DB6 · human melatonin receptor MT1 - Gi1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P48039 · AlphaFold monomer V2.0 prediction for melatonin receptor type 1A (P48039) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.78
- P63212 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain C 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 P63096
- Every structure of UniProt P63212
- Every structure of UniProt P48039
- Elsewhere: RCSB PDB 7DB6 · PDBe 7DB6 · UniProt P63096 · UniProt P63212 · UniProt P48039
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