Research workbench
Structure basis of lipopolysaccharide biogenesis
Analyse Structure basis of lipopolysaccharide biogenesis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N4R
- Type
- protein
- Length
- 1,367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps-assembly protein lptd; Lps-assembly lipoprotein lpte
- UniProt
- Q8ZRW0, Q8ZQZ7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 532 | 5% helix, 55% strand | Q8ZRW0 |
| B, D | Lps-assembly lipoprotein lpte | protein | 151 | 34% helix, 36% strand | Q8ZQZ7 |
| C | Lps-assembly protein lptd | protein | 533 | 5% helix, 56% strand | Q8ZRW0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
- CAC · Cacodylate ion · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.85 | 0.92 | 76 | empty |
| 2 | 452 | 0.84 | 0.92 | 68 | empty |
| 3 | 264 | 0.80 | 0.92 | 41 | empty |
| 4 | 258 | 0.78 | 0.91 | 39 | empty |
| 5 | 659 | 0.77 | 0.83 | 68 | CAC |
Interfaces
3 interfaces between chains.
- A–B · 3516 Ų buried · 49 hydrogen bonds · protein-protein
- C–D · 3490 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 4N4R · Structure basis of lipopolysaccharide biogenesis · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZRW0 · AlphaFold monomer V2.0 prediction for lps-assembly protein lptd (Q8ZRW0) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q8ZQZ7 · AlphaFold monomer V2.0 prediction for lps-assembly lipoprotein lpte (Q8ZQZ7) · a predicted model of the same protein · chain B 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 Q8ZRW0
- Every structure of UniProt Q8ZQZ7
- Elsewhere: RCSB PDB 4N4R · PDBe 4N4R · UniProt Q8ZRW0 · UniProt Q8ZQZ7
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