Research workbench
Melatonin RECEPTOR1-2-iodomelatonin-gicomplex
Analyse Melatonin RECEPTOR1-2-iodomelatonin-gicomplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VGY
- Type
- protein
- Length
- 1,121 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melatonin receptor type 1A; Guanine nucleotide-binding protein G(I) subunit alpha-1…
- UniProt
- P48039, P63096, P54311, P63212
- Ligands
- CLR, ML2
- Pockets
- 17 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melatonin receptor type 1A | protein | 281 | 74% helix, 3% strand | P48039 |
| B | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 46% helix, 15% strand | P63096 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 46% strand | P54311 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 60% helix, 0% strand | P63212 |
| E | SCFV16 | protein | 231 | 1% helix, 45% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- ML2 · N-[2-(2-iodo-5-methoxy-1H-indol-3-yl)ethyl]acetamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.83 | 0.86 | 66 | empty |
| 2 | 151 | 0.79 | 0.96 | 25 | ML2 |
| 3 | 840 | 0.73 | 0.78 | 93 | empty |
| 4 | 202 | 0.54 | 0.78 | 34 | empty |
| 5 | 102 | 0.51 | 0.83 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2169 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1009 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 573 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 444 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7VGY · Melatonin receptor1-2-Iodomelatonin-Gicomplex · the same entry in another collection · chain E against E, TM-score 1.00
- P54311 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.93
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain B against A, TM-score 0.84
- 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 D against A, TM-score 0.67
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 P63096
- Every structure of UniProt P54311
- Every structure of UniProt P63212
- Elsewhere: RCSB PDB 7VGY · PDBe 7VGY · UniProt P48039 · UniProt P63096 · UniProt P54311 · UniProt P63212
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