Research workbench
The lps transporter lptde from yersinia pestis, core complex
Analyse The lps transporter lptde from yersinia pestis, core complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IXM
- Type
- protein
- Length
- 2,740 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lps-assembly protein lptd; Lps-assembly lipoprotein lpte
- UniProt
- Q8ZIK3, Q7CJV2
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 8 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lps-assembly protein lptd | protein | 543 | 6% helix, 57% strand | Q8ZIK3 |
| B | Lps-assembly lipoprotein lpte | protein | 141 | 33% helix, 37% strand | Q7CJV2 |
| C | Lps-assembly protein lptd | protein | 541 | 5% helix, 57% strand | Q8ZIK3 |
| D | Lps-assembly lipoprotein lpte | protein | 146 | 31% helix, 38% strand | Q7CJV2 |
| E | Lps-assembly protein lptd | protein | 538 | 4% helix, 56% strand | Q8ZIK3 |
| F | Lps-assembly lipoprotein lpte | protein | 145 | 32% helix, 35% strand | Q7CJV2 |
| G | Lps-assembly protein lptd | protein | 539 | 4% helix, 58% strand | Q8ZIK3 |
| H | Lps-assembly lipoprotein lpte | protein | 147 | 34% helix, 37% strand | Q7CJV2 |
Ligands and binding sites
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 21 copies · chains A, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.88 | 0.90 | 132 | empty |
| 2 | 1031 | 0.88 | 0.90 | 138 | empty |
| 3 | 635 | 0.86 | 0.91 | 85 | empty |
| 4 | 645 | 0.84 | 0.89 | 90 | empty |
| 5 | 488 | 0.84 | 0.91 | 70 | empty |
Interfaces
8 interfaces between chains.
- G–H · 3427 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 3410 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 3333 Ų buried · 43 hydrogen bonds · protein-protein
- E–F · 3279 Ų buried · 36 hydrogen bonds · protein-protein
- E–G · 772 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q8ZIK3
- Every structure of UniProt Q7CJV2
- Elsewhere: RCSB PDB 5IXM · PDBe 5IXM · UniProt Q8ZIK3 · UniProt Q7CJV2
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