Research workbench
The missing part of the bacterial mexab-oprm system: structural determination of the multidrug exporter mexb
Analyse The missing part of the bacterial mexab-oprm system: structural determination… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V50
- Type
- protein
- Length
- 6,105 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Multidrug resistance protein mexb
- UniProt
- P52002
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multidrug resistance protein mexb | protein | 1005 | 49% helix, 18% strand | P52002 |
| B, C, F | Multidrug resistance protein mexb | protein | 1030 | 51% helix, 17% strand | P52002 |
| D | Multidrug resistance protein mexb | protein | 998 | 50% helix, 17% strand | P52002 |
| E | Multidrug resistance protein mexb | protein | 1012 | 52% helix, 17% strand | P52002 |
Ligands and binding sites
- LMT · Dodecyl-beta-D-maltoside · additive · 8 copies · chains A, B, D, E
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 | 1133 | 0.89 | 0.91 | 129 | empty |
| 2 | 862 | 0.87 | 0.89 | 97 | LMT |
| 3 | 973 | 0.87 | 0.88 | 105 | empty |
| 4 | 546 | 0.87 | 0.93 | 78 | empty |
| 5 | 762 | 0.86 | 0.89 | 77 | empty |
Interfaces
8 interfaces between chains.
- A–B · 3517 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 3482 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 3373 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 3345 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 3166 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2V50 · The Missing Part of the Bacterial MexAB-OprM System: Structural determination of the… · the same entry in another collection · chain F against F, TM-score 1.00
- P52002 · AlphaFold monomer V2.0 prediction for multidrug resistance protein mexb (P52002) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P52002
- Elsewhere: RCSB PDB 2V50 · PDBe 2V50 · UniProt P52002
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