Research workbench
Structure of the macab-tolc ABC-type tripartite multidrug efflux pump- macb section
Analyse Structure of the macab-tolc ABC-type tripartite multidrug efflux pump- macb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NIL
- Type
- protein
- Length
- 4,582 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein tolc; Macrolide export protein maca; Macrolide export…
- EC
- 3.6.3.-
- UniProt
- P02930, P75830, P75831
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein tolc | protein | 428 | 68% helix, 13% strand | P02930 |
| D, E, F, G, H, I | Macrolide export protein maca | protein | 340 | 24% helix, 26% strand | P75830 |
| J, K | Macrolide export ATP-BINDING/PERMEASE protein macb (EC 3.6.3.-) | protein | 629 | 48% helix, 14% strand | P75831 |
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 | 1127 | 0.81 | 0.82 | 138 | empty |
| 2 | 600 | 0.77 | 0.83 | 82 | empty |
| 3 | 558 | 0.76 | 0.83 | 71 | empty |
| 4 | 772 | 0.73 | 0.78 | 87 | empty |
| 5 | 53 | 0.72 | 0.98 | 18 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2213 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 2196 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2190 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2082 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 2077 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5NIL · Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump-MacB section · the same entry in another collection · chain K against K, TM-score 1.00
- P75830 · AlphaFold monomer V2.0 prediction for macrolide export protein maca (P75830) · a predicted model of the same protein · chain D 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 P02930
- Every structure of UniProt P75830
- Every structure of UniProt P75831
- Elsewhere: RCSB PDB 5NIL · PDBe 5NIL · UniProt P02930 · UniProt P75830 · UniProt P75831
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