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Minocycline bound structure of bacterial efflux pump.
Analyse Minocycline 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
- 5ENT
- Type
- protein
- Length
- 2,218 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
- MIY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 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 | 34% helix, 36% strand | P31224 |
| C | Multidrug efflux pump subunit ACRB,MULTIDRUG efflux pump subunit acrb | protein | 581 | 33% helix, 34% strand | P31224 |
| D | Darpin | protein | 161 | 52% helix, 2% strand | — |
| E | Darpin | protein | 156 | 53% helix, 0% strand | — |
| F | Darpin | protein | 162 | 52% helix, 0% strand | — |
Ligands and binding sites
- MIY · (4s,4as,5ar,12as)-4,7-bis(dimethylamino)-3,10,12,12A-tetrahydroxy-1,11-dioxo-1,4,4A,5,5A,6,11,12A-octahydrotetracene-2-carboxamide · ligand · chains C
- PEG · Di(hydroxyethyl)ether · additive · 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 | 1085 | 0.87 | 0.89 | 117 | empty |
| 2 | 931 | 0.87 | 0.89 | 93 | empty |
| 3 | 1117 | 0.86 | 0.87 | 123 | empty |
| 4 | 1177 | 0.83 | 0.84 | 88 | MIY |
| 5 | 1114 | 0.83 | 0.84 | 103 | empty |
Interfaces
9 interfaces between chains.
- B–C · 3130 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3050 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2678 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 910 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 888 Ų buried · 11 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 5ENT · PDBe 5ENT · UniProt P31224
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