Research workbench
Crystal structure of the K. pneumoniae LPXH/JH-lph-41 complex
Analyse Crystal structure of the K. pneumoniae LPXH/JH-lph-41 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WII
- Type
- protein
- Length
- 238 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
- U2V, MN
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-2,3-diacylglucosamine hydrolase (EC 3.6.1.54) | protein | 238 | 35% helix, 24% strand | A0A1S0WIC1 |
Ligands and binding sites
- U2V · 5-({[4-({4-[3-chloro-5-(trifluoromethyl) phenyl]piperazin-1-yl}sulfonyl) phenyl]carbamoyl}amino)-N-hydroxypentanamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.57 | 0.81 | 21 | U2V |
| 2 | 77 | 0.41 | 0.79 | 16 | DMS |
Compared structures
- 6WII · Crystal structure of the K. pneumoniae LpxH/JH-LPH-41 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 6WII · PDBe 6WII · UniProt A0A1S0WIC1
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