MolNFT v1 · #105848 · protein
Crystal structure of the lipopolysaccharide assembly complex lptd-lpte from the escherichia COLI outer membrane
4RHB · Lps-assembly protein lptd: “Crystal structure of the lipopolysaccharide assembly complex lptd-lpte from the escherichia COLI outer…”. X-ray diffraction, 2 ligands (NA, CL), 16 pockets (best druggability 0.88). MolNFT v1 #105848 on…
- PDB
- 4RHB
- Type
- protein
- Length
- 1,413 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
- P31554, P0ADC1
- Ligands
- NA, CL
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 556 | 8% helix, 53% strand | P31554 |
| B, D | Lps-assembly lipoprotein lpte | protein | 150 | 31% helix, 31% strand | P0ADC1 |
| C | Lps-assembly protein lptd | protein | 557 | 8% helix, 54% strand | P31554 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.88 | 0.90 | 135 | empty |
| 2 | 1170 | 0.88 | 0.90 | 141 | empty |
| 3 | 822 | 0.80 | 0.83 | 85 | empty |
| 4 | 555 | 0.79 | 0.85 | 72 | empty |
| 5 | 303 | 0.78 | 0.90 | 48 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3630 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 3610 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RHB · Crystal structure of the lipopolysaccharide assembly complex LptD-LptE from the… · the same entry in another collection · chain A against A, TM-score 1.00
- P31554 · AlphaFold monomer V2.0 prediction for lps-assembly protein lptd (P31554) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0ADC1 · AlphaFold monomer V2.0 prediction for lps-assembly lipoprotein lpte (P0ADC1) · 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 P31554
- Every structure of UniProt P0ADC1
- Elsewhere: RCSB PDB 4RHB · PDBe 4RHB · UniProt P31554 · UniProt P0ADC1
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