Research workbench
Crystal structure of the klebsiella pneumoniae lpxh-lipid X complex
Analyse Crystal structure of the klebsiella pneumoniae lpxh-lipid X complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PH9
- Type
- protein
- Length
- 243 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-2,3-diacylglucosamine hydrolase
- EC
- 3.6.1.54
- UniProt
- A0A1S0WIC1
- Ligands
- LP5, MN, CA
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54) | protein | 243 | 39% helix, 23% strand | A0A1S0WIC1 |
Ligands and binding sites
- LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A
- CA · Calcium ion · metal · chains A
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.67 | 0.80 | 43 | LP5, PG4 |
| 2 | 82 | 0.37 | 0.76 | 17 | empty |
| 3 | 57 | 0.33 | 0.77 | 25 | empty |
Compared structures
- 6PH9 · Crystal Structure of the Klebsiella pneumoniae LpxH-lipid X complex · 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 A0A1S0WIC1
- Elsewhere: RCSB PDB 6PH9 · PDBe 6PH9 · UniProt A0A1S0WIC1
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