MolNFT v1 · #190704 · protein
Cryo-EM structure of apo-state mrgd-gi complex (local)
7Y13 · Soluble cytochrome B562,MAS-related G-protein coupled…: “Cryo-EM structure of apo-state mrgd-gi complex (local)”. Electron microscopy, 1 ligand (PLM), 3 pockets (best druggability 0.52). MolNFT v1 #190704 on GenesisL1: 3D structure…
- PDB
- 7Y13
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble cytochrome B562,MAS-related G-protein coupled receptor member D
- UniProt
- Q8TDS7
- Ligands
- PLM
- Pockets
- 3 · best druggability 0.52
Structure
electron microscopy · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Soluble cytochrome B562,MAS-related G-protein coupled receptor member D | protein | 264 | 78% helix, 0% strand | Q8TDS7 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 7 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.52 | 0.77 | 21 | empty |
| 2 | 163 | 0.52 | 0.79 | 24 | empty |
| 3 | 135 | 0.44 | 0.76 | 25 | PLM |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7Y13 · Cryo-EM structure of apo-state MrgD-Gi complex (local) · the same entry in another collection · chain R against R, TM-score 1.00
- Q8TDS7 · AlphaFold monomer V2.0 prediction for mas-related G-protein coupled receptor member D… · a predicted model of the same protein · chain R against A, TM-score 0.92
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 Q8TDS7
- Elsewhere: RCSB PDB 7Y13 · PDBe 7Y13 · UniProt Q8TDS7
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