MolNFT v1 · #156889 · protein
Cryo-EM structure of vanadate-trapped E.COLI LPTB2FGC
6MI8 · Lipopolysaccharide export system ATP-binding protein lptb: “Cryo-EM structure of vanadate-trapped E.COLI LPTB2FGC”. Electron microscopy, 1 ligand (AOV), 17 pockets (best druggability 0.89). MolNFT v1 #156889 on GenesisL1: 3D…
- PDB
- 6MI8
- Type
- protein
- Length
- 911 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
- 17 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 63% 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 | 39% helix, 23% strand | P0A9V1 |
| F | Lipopolysaccharide export system permease protein lptf | protein | 213 | 74% helix, 0% strand | P0AF98 |
| G | Lipopolysaccharide export system permease protein lptg | protein | 228 | 77% 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
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.89 | 0.91 | 131 | AOV |
| 2 | 604 | 0.77 | 0.83 | 64 | empty |
| 3 | 244 | 0.70 | 0.86 | 39 | empty |
| 4 | 335 | 0.62 | 0.78 | 35 | empty |
| 5 | 67 | 0.59 | 0.90 | 12 | AOV |
Interfaces
6 interfaces between chains.
- F–G · 1594 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 1062 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 1043 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 194 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6MI8 · Cryo-EM Structure of vanadate-trapped E.coli LptB2FGC · 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 0.84
- 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 6MI8 · PDBe 6MI8 · UniProt P0A9V1 · UniProt P0AF98 · UniProt P0ADC6
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