Research workbench
Vanadate trapped cryo-EM structure of E.COLI LPTB2FG transporter
Analyse Vanadate trapped cryo-EM structure of E.COLI LPTB2FG transporter in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MHZ
- Type
- protein
- Length
- 908 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide export system ATP-binding protein lptb; Lipopolysaccharide export…
- EC
- 3.6.3.-
- UniProt
- P0A9V1, P0AF98, P0ADC6
- Ligands
- AOV
- Pockets
- 14 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 235 | 37% helix, 22% strand | P0A9V1 |
| F | Lipopolysaccharide export system permease protein lptf | protein | 210 | 70% helix, 0% strand | P0AF98 |
| G | Lipopolysaccharide export system permease protein lptg | protein | 228 | 64% helix, 0% strand | P0ADC6 |
Ligands and binding sites
- AOV · Adp orthovanadate · ligand · 2 copies · chains A, B, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.86 | 0.93 | 85 | empty |
| 2 | 235 | 0.80 | 0.93 | 31 | empty |
| 3 | 913 | 0.77 | 0.80 | 90 | empty |
| 4 | 205 | 0.67 | 0.85 | 33 | empty |
| 5 | 81 | 0.67 | 0.93 | 31 | AOV |
Interfaces
6 interfaces between chains.
- F–G · 1596 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1186 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 1080 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 795 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 182 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6MHZ · Vanadate trapped Cryo-EM Structure of E.coli LptB2FG Transporter · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9V1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system ATP-binding… · a predicted model of the same protein · chain A against A, TM-score 0.92
- P0AF98 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain F against A, TM-score 0.83
- P0ADC6 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain G against A, TM-score 0.83
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 P0A9V1
- Every structure of UniProt P0AF98
- Every structure of UniProt P0ADC6
- Elsewhere: RCSB PDB 6MHZ · PDBe 6MHZ · UniProt P0A9V1 · UniProt P0AF98 · UniProt P0ADC6
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