Research workbench
Cryo-EM structure of mechanosensitive channel mscs in pc-18:1 nanodiscs
Analyse Cryo-EM structure of mechanosensitive channel mscs in pc-18:1 nanodiscs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VYK
- Type
- protein
- Length
- 1,869 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mechanosensitive channel mscs
- UniProt
- C3SVH2
- Ligands
- PCW
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 1 distinct chain · 51% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | Mechanosensitive channel mscs | protein | 267 | 51% helix, 22% strand | C3SVH2 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 7 copies · chains A, G, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.74 | 0.87 | 28 | empty |
| 2 | 1190 | 0.74 | 0.77 | 55 | empty |
| 3 | 552 | 0.68 | 0.77 | 67 | PCW |
| 4 | 520 | 0.67 | 0.77 | 54 | empty |
| 5 | 503 | 0.63 | 0.76 | 106 | empty |
Interfaces
14 interfaces between chains.
- A–B · 3096 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 3033 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 2958 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2956 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 2936 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6VYK · Cryo-EM structure of mechanosensitive channel MscS in PC-18:1 nanodiscs · 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
- Every structure of UniProt C3SVH2
- Elsewhere: RCSB PDB 6VYK · PDBe 6VYK · UniProt C3SVH2
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