MolNFT v1 · #145602 · protein
Single particles cryo-EM structure of acrb D407A associated with lipid bilayer at 3.0 ångström
6CSX · Multidrug efflux pump subunit acrb: “Single particles cryo-EM structure of acrb D407A associated with lipid bilayer at 3.0 ångström”. Electron microscopy, 2 ligands (PTY, D12), 20 pockets (best druggability 0.89). MolNFT v1 #145602…
- PDB
- 6CSX
- Type
- protein
- Length
- 2,999 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, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Multidrug efflux pump subunit acrb | protein | 1019 | 47% helix, 19% strand | P31224 |
| C | Multidrug efflux pump subunit acrb | protein | 1015 | 43% helix, 17% strand | P31224 |
| A | Multidrug efflux pump subunit acrb | protein | 965 | 46% helix, 20% strand | P31224 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 18 copies · chains B, C, A
- D12 · Dodecane · ligand · chains B
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 | 1089 | 0.89 | 0.91 | 133 | empty |
| 2 | 992 | 0.88 | 0.89 | 129 | empty |
| 3 | 1127 | 0.87 | 0.88 | 137 | empty |
| 4 | 796 | 0.76 | 0.81 | 96 | empty |
| 5 | 378 | 0.76 | 0.86 | 32 | empty |
Interfaces
3 interfaces between chains.
- B–A · 3508 Ų buried · 34 hydrogen bonds · protein-protein
- C–A · 3249 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3078 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6CSX · Single particles Cryo-EM structure of AcrB D407A associated with lipid bilayer at 3.0… · 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 6CSX · PDBe 6CSX · UniProt P31224
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