Research workbench
Structure of the essential inner membrane lipopolysaccharide-pbga complex
Analyse Structure of the essential inner membrane lipopolysaccharide-pbga complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XLP
- Type
- protein
- Length
- 586 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps binding protein
- UniProt
- C3T3G2
- Ligands
- OLB, VJ4, VJ1, 3PE, KDO, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps binding protein | protein | 586 | 53% helix, 12% strand | C3T3G2 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 8 copies · chains A
- VJ4 · 2-deoxy-2-{[(1S,3R)-1-hydroxy-3-(pentanoyloxy) undecyl]amino}-4-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- VJ1 · 2-deoxy-3-O-[(1R,3R)-1,3-dihydroxytetradecyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-1-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · chains A
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.80 | 0.83 | 68 | PG4, 3PE |
| 2 | 75 | 0.63 | 0.92 | 28 | empty |
| 3 | 50 | 0.60 | 0.92 | 21 | PG4 |
| 4 | 212 | 0.56 | 0.78 | 23 | OLB |
| 5 | 81 | 0.50 | 0.83 | 16 | OLB |
Compared structures
- 6XLP · Structure of the essential inner membrane lipopolysaccharide-PbgA complex · the same entry in another collection · chain A against A, TM-score 1.00
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 C3T3G2
- Elsewhere: RCSB PDB 6XLP · PDBe 6XLP · UniProt C3T3G2
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