Research workbench
Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of acrb
Analyse Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BAJ
- Type
- protein
- Length
- 3,042 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit acrb
- UniProt
- P31224
- Ligands
- PTY, D12
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Multidrug efflux pump subunit acrb | protein | 1024 | 46% helix, 15% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1023 | 44% helix, 17% strand | P31224 |
| A | Multidrug efflux pump subunit acrb | protein | 995 | 44% helix, 15% strand | P31224 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 31 copies · chains B, C, A
- D12 · Dodecane · ligand · 11 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.89 | 0.93 | 112 | empty |
| 2 | 959 | 0.84 | 0.86 | 91 | empty |
| 3 | 1140 | 0.84 | 0.85 | 145 | empty |
| 4 | 553 | 0.83 | 0.89 | 84 | empty |
| 5 | 781 | 0.78 | 0.82 | 110 | empty |
Interfaces
3 interfaces between chains.
- B–A · 3504 Ų buried · 34 hydrogen bonds · protein-protein
- C–A · 3247 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2942 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6BAJ · Cryo-EM structure of lipid bilayer in the native cell membrane nanoparticles of AcrB · the same entry in another collection · chain B against B, TM-score 1.00
- P31224 · AlphaFold monomer V2.0 prediction for multidrug efflux pump subunit acrb (P31224) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P31224
- Elsewhere: RCSB PDB 6BAJ · PDBe 6BAJ · UniProt P31224
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