Research workbench
Nucleotide-free cryo-EM structure of E.COLI LPTB2FGC
Analyse Nucleotide-free cryo-EM structure of E.COLI LPTB2FGC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MI7
- Type
- protein
- Length
- 931 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide export system permease protein lptf; Lipopolysaccharide export system…
- EC
- 3.6.3.-
- UniProt
- P0AF98, P0ADC6, P0A9V1, P0ADV9
- Ligands
- PGT
- Pockets
- 14 · best druggability 0.69
Structure
electron microscopy · 4 distinct chains · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Lipopolysaccharide export system permease protein lptf | protein | 217 | 58% helix, 0% strand | P0AF98 |
| G | Lipopolysaccharide export system permease protein lptg | protein | 230 | 57% helix, 0% strand | P0ADC6 |
| A, B | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 230 | 27% helix, 21% strand | P0A9V1 |
| C | Lipopolysaccharide export system protein lptc | protein | 24 | 67% helix, 0% strand | P0ADV9 |
Ligands and binding sites
- PGT · (1S)-2-{[{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl stearate · ligand · chains F, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.69 | 0.81 | 52 | empty |
| 2 | 429 | 0.68 | 0.80 | 49 | empty |
| 3 | 833 | 0.67 | 0.73 | 72 | empty |
| 4 | 611 | 0.66 | 0.76 | 48 | empty |
| 5 | 393 | 0.63 | 0.78 | 39 | empty |
Interfaces
6 interfaces between chains.
- F–B · 1093 Ų buried · 11 hydrogen bonds · protein-protein
- G–A · 923 Ų buried · 8 hydrogen bonds · protein-protein
- F–C · 568 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 413 Ų buried · 2 hydrogen bonds · protein-protein
- F–G · 364 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MI7 · Nucleotide-free Cryo-EM Structure of E.coli LptB2FGC · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.95
- 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 0.95
- 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
- P0ADV9 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system protein lptc… · a predicted model of the same protein · chain C against A, TM-score 0.58
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 P0AF98
- Every structure of UniProt P0ADC6
- Every structure of UniProt P0A9V1
- Every structure of UniProt P0ADV9
- Elsewhere: RCSB PDB 6MI7 · PDBe 6MI7 · UniProt P0AF98 · UniProt P0ADC6 · UniProt P0A9V1 · UniProt P0ADV9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.