MolNFT v1 · #189466 · protein
MT1-remalteon-gi complex
7VGZ · Melatonin receptor type 1A: “MT1-remalteon-gi complex”. Electron microscopy, 2 ligands (JEV, CLR), 12 pockets (best druggability 0.83). MolNFT v1 #189466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VGZ
- Type
- protein
- Length
- 1,125 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
- JEV, CLR
- Pockets
- 12 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Melatonin receptor type 1A | protein | 285 | 77% helix, 3% strand | P48039 |
| C | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 47% helix, 14% strand | P63096 |
| D | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 45% strand | P54311 |
| E | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 58% helix, 0% strand | P63212 |
| F | SCFV16 | protein | 231 | 4% helix, 48% strand | — |
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 B
- CLR · Cholesterol · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.83 | 0.86 | 62 | empty |
| 2 | 168 | 0.81 | 0.96 | 25 | JEV |
| 3 | 892 | 0.74 | 0.78 | 87 | empty |
| 4 | 110 | 0.57 | 0.85 | 26 | empty |
| 5 | 174 | 0.53 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2202 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1144 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 996 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 615 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7VGZ · MT1-remalteon-Gi complex · the same entry in another collection · chain F against F, 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 D 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 B 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 C 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 E against A, TM-score 0.63
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 7VGZ · PDBe 7VGZ · UniProt P48039 · UniProt P63096 · UniProt P54311 · UniProt P63212
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