Research workbench
MBX2319 bound structure of bacterial efflux pump.
Analyse MBX2319 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
- 5ENO
- Type
- protein
- Length
- 2,215 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
- 5QG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 29% 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, 35% strand | P31224 |
| C | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 577 | 33% helix, 33% strand | P31224 |
| D, F | Darpin | protein | 162 | 52% helix, 0% strand | — |
| E | Darpin | protein | 156 | 52% helix, 0% strand | — |
Ligands and binding sites
- 5QG · 3,3-dimethyl-8-morpholin-4-yl-6-(2-phenylethylsulfanyl)-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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.87 | 0.89 | 121 | empty |
| 2 | 1186 | 0.87 | 0.89 | 133 | empty |
| 3 | 1112 | 0.86 | 0.87 | 126 | empty |
| 4 | 1140 | 0.85 | 0.86 | 130 | empty |
| 5 | 1054 | 0.85 | 0.86 | 93 | 5QG |
Interfaces
9 interfaces between chains.
- B–C · 3151 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 3011 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2643 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 932 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 882 Ų buried · 9 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 5ENO · PDBe 5ENO · UniProt P31224
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