MolNFT v1 · #122634 · protein
The lps transporter lptde from klebsiella pneumoniae, full-length
5IV9 · Lps-assembly protein lptd: “The lps transporter lptde from klebsiella pneumoniae, full-length”. X-ray diffraction, 9 pockets (best druggability 0.86). MolNFT v1 #122634 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IV9
- Type
- protein
- Length
- 908 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps-assembly protein lptd; Lps-assembly lipoprotein lpte
- UniProt
- C4T9I0, A0A0J4W1Y0
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 758 | 3% helix, 54% strand | C4T9I0 |
| B | Lps-assembly lipoprotein lpte | protein | 150 | 33% helix, 35% strand | A0A0J4W1Y0 |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.86 | 0.88 | 95 | empty |
| 2 | 1034 | 0.84 | 0.85 | 139 | empty |
| 3 | 263 | 0.78 | 0.91 | 44 | empty |
| 4 | 260 | 0.72 | 0.86 | 47 | empty |
| 5 | 250 | 0.69 | 0.85 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 3396 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5IV9 · The LPS Transporter LptDE from Klebsiella pneumoniae, full-length · 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 C4T9I0
- Every structure of UniProt A0A0J4W1Y0
- Elsewhere: RCSB PDB 5IV9 · PDBe 5IV9 · UniProt C4T9I0 · UniProt A0A0J4W1Y0
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