MolNFT v1 · #122635 · protein
The lps transporter lptde from pseudomonas aeruginosa, core complex
5IVA · Lps-assembly protein lptd: “The lps transporter lptde from pseudomonas aeruginosa, core complex”. X-ray diffraction, 13 pockets (best druggability 0.81). MolNFT v1 #122635 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IVA
- Type
- protein
- Length
- 731 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
- Q9I5U2, A0A0A8RAG8
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 579 | 5% helix, 55% strand | Q9I5U2 |
| B | Lps-assembly lipoprotein lpte | protein | 152 | 29% helix, 36% strand | A0A0A8RAG8 |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.81 | 0.96 | 35 | empty |
| 2 | 392 | 0.79 | 0.89 | 52 | empty |
| 3 | 518 | 0.78 | 0.85 | 70 | empty |
| 4 | 228 | 0.69 | 0.85 | 43 | empty |
| 5 | 172 | 0.63 | 0.85 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 3260 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5IVA · The LPS Transporter LptDE from Pseudomonas aeruginosa, core complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I5U2 · AlphaFold monomer V2.0 prediction for lps-assembly protein lptd (Q9I5U2) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q9I5U2
- Every structure of UniProt A0A0A8RAG8
- Elsewhere: RCSB PDB 5IVA · PDBe 5IVA · UniProt Q9I5U2 · UniProt A0A0A8RAG8
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