Research workbench
Cryo-EM structure of LPTB2FGC in complex with lipopolysaccharide
Analyse Cryo-EM structure of LPTB2FGC in complex with lipopolysaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S8N
- Type
- protein
- Length
- 970 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide ABC transporter, ATP-binding protein lptb; Lipopolysaccharide export…
- UniProt
- E7T9E6, D2A8C1, P0AFA1, A0A2S4N3I3
- Ligands
- DCQ, LMN, L0W
- Pockets
- 7 · best druggability 0.71
Structure
electron microscopy · 5 distinct chains · 43% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 239 | 23% helix, 18% strand | E7T9E6 |
| B | Lipopolysaccharide ABC transporter, ATP-binding protein lptb | protein | 238 | 31% helix, 24% strand | E7T9E6 |
| C | Lipopolysaccharide export system protein lptc | protein | 24 | 71% helix, 0% strand | D2A8C1 |
| F | Lipopolysaccharide export system permease protein lptf | protein | 239 | 59% helix, 0% strand | P0AFA1 |
| G | Inner membrane protein yjgq | protein | 230 | 57% helix, 0% strand | A0A2S4N3I3 |
Ligands and binding sites
- DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · 2 copies · chains B, F, G
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains C, F, G
- L0W · lipopolysaccharide fragment · ligand · chains C, F, G
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.71 | 0.75 | 102 | LMN, LMT |
| 2 | 444 | 0.70 | 0.81 | 47 | empty |
| 3 | 119 | 0.60 | 0.85 | 22 | empty |
| 4 | 469 | 0.59 | 0.74 | 46 | empty |
| 5 | 264 | 0.55 | 0.76 | 28 | empty |
Interfaces
7 interfaces between chains.
- A–G · 990 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 968 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 653 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 615 Ų buried · 0 hydrogen bonds · protein-protein
- F–G · 279 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 6S8N · Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFA1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain F against A, TM-score 0.98
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 E7T9E6
- Every structure of UniProt D2A8C1
- Every structure of UniProt P0AFA1
- Every structure of UniProt A0A2S4N3I3
- Elsewhere: RCSB PDB 6S8N · PDBe 6S8N · UniProt E7T9E6 · UniProt D2A8C1 · UniProt P0AFA1 · UniProt A0A2S4N3I3
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