Research workbench
Fusidic acid bound structure of bacterial efflux pump.
Analyse Fusidic acid bound structure of bacterial efflux pump. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B8S
- Type
- protein
- Length
- 2,219 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb; Darpin
- UniProt
- P31224
- Ligands
- FUA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 587 | 35% helix, 36% strand | P31224 |
| B | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 576 | 33% helix, 35% strand | P31224 |
| C | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 589 | 35% helix, 33% strand | P31224 |
| D | Darpin | protein | 157 | 52% helix, 0% strand | — |
| E, F | Darpin | protein | 155 | 53% helix, 0% strand | — |
Ligands and binding sites
- FUA · Fusidic acid · ligand · chains 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.88 | 0.89 | 126 | empty |
| 2 | 985 | 0.87 | 0.89 | 112 | empty |
| 3 | 899 | 0.86 | 0.88 | 141 | empty |
| 4 | 987 | 0.83 | 0.84 | 90 | empty |
| 5 | 699 | 0.82 | 0.86 | 117 | empty |
Interfaces
9 interfaces between chains.
- B–C · 3091 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3036 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2673 Ų buried · 30 hydrogen bonds · protein-protein
- C–E · 920 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 865 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7B8S · Fusidic acid bound structure of bacterial efflux pump. · the same entry in another collection · chain F against F, 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 B against A, TM-score 0.94
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 7B8S · PDBe 7B8S · UniProt P31224
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