Research workbench
Nachbac in lipid nanodisc
Analyse Nachbac in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VWX
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH1501 protein
- UniProt
- Q9KCR8
- Ligands
- POV, NA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | BH1501 protein | protein | 225 | 71% helix, 0% strand | Q9KCR8 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 8 copies · chains A, F, D, E
- NA · Sodium ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.85 | 0.86 | 93 | NA |
| 2 | 132 | 0.50 | 0.79 | 22 | empty |
| 3 | 126 | 0.48 | 0.79 | 20 | empty |
| 4 | 157 | 0.47 | 0.77 | 20 | empty |
| 5 | 117 | 0.46 | 0.78 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–F · 1625 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1619 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1617 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1616 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6VWX · NaChBac in 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
- Every structure of UniProt Q9KCR8
- Elsewhere: RCSB PDB 6VWX · PDBe 6VWX · UniProt Q9KCR8
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