MolNFT v1 · #187469 · protein
Chrmine in MSP1E3D1 lipid nanodisc
7SFK: “Chrmine in MSP1E3D1 lipid nanodisc”. Electron microscopy, 2 ligands (PEE, RET), 17 pockets (best druggability 0.84). MolNFT v1 #187469 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7SFK
- Type
- protein
- Length
- 852 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chrmine
- Ligands
- PEE, RET
- Pockets
- 17 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 69% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Chrmine | protein | 284 | 69% helix, 1% strand | — |
Ligands and binding sites
- PEE · 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine · ligand · 21 copies · chains A, C, B
- RET · Retinal · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.84 | 0.96 | 31 | RET |
| 2 | 197 | 0.82 | 0.95 | 24 | RET |
| 3 | 204 | 0.81 | 0.95 | 27 | RET |
| 4 | 335 | 0.77 | 0.88 | 54 | empty |
| 5 | 276 | 0.75 | 0.87 | 26 | PEE |
Interfaces
3 interfaces between chains.
- A–C · 1600 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1574 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1563 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 cofactor, 3 modified (retinal Schiff base, nonstandard).
Compared structures
- 7SFK · ChRmine in MSP1E3D1 lipid nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7SFK · PDBe 7SFK
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