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MBX2931 bound structure of bacterial efflux pump.
Analyse MBX2931 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
- 5ENP
- Type
- protein
- Length
- 2,215 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Escherichia coli (strain K12); Escherichia coli K-12; synthetic construct
- Molecule
- Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB; DARPin
- UniProt
- P31224
- Ligands
- 5QF
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · resolution 1.9 · 6 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB | protein | 580 | 33% helix, 36% strand | P31224 |
| B | Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB | protein | 578 | 33% helix, 36% strand | P31224 |
| C | Multidrug efflux pump subunit AcrB,Multidrug efflux pump subunit AcrB | protein | 578 | 33% helix, 34% strand | P31224 |
| D | DARPin | protein | 161 | 53% helix, 0% strand | — |
| E | DARPin | protein | 156 | 53% helix, 0% strand | — |
| F | DARPin | protein | 162 | 52% helix, 0% strand | — |
Ligands and binding sites
- 5QF · 6-[2-(3,4-dimethoxyphenyl)ethylsulfanyl]-8-[4-(2-methoxyethyl)piperazin-1-yl]-3,3-dimethyl-1,4-dihydropyrano[3,4-c]pyridine-5-carbonitrile · 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.88 | 0.91 | 111 | empty |
| 2 | 1026 | 0.87 | 0.89 | 119 | empty |
| 3 | 1065 | 0.86 | 0.87 | 119 | empty |
| 4 | 609 | 0.85 | 0.90 | 105 | empty |
| 5 | 588 | 0.81 | 0.87 | 47 | empty |
Interfaces
9 interfaces between chains.
- B–C · 3115 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2940 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2643 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 916 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 872 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 5ENP · PDBe 5ENP · UniProt P31224
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