Research workbench
Structure of lpxi D225A mutant
Analyse Structure of lpxi D225A mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J6E
- Type
- protein
- Length
- 273 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-2,3-diacylglucosamine pyrophosphatase lpxi
- EC
- 3.6.1.54
- UniProt
- B8GWR0
- Ligands
- UDG
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-2,3-diacylglucosamine pyrophosphatase lpxi (EC 3.6.1.54) | protein | 273 | 41% helix, 18% strand | B8GWR0 |
Ligands and binding sites
- UDG · (2R,3R,4R,5S,6R)-2-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)-3-{[(3R)-3-hydroxytetradecanoyl]amino}tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate · ligand · 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 | 781 | 0.80 | 0.83 | 75 | UDG |
| 2 | 111 | 0.47 | 0.79 | 19 | empty |
Compared structures
- 4J6E · Structure of LPXI D225A Mutant · 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 B8GWR0
- Elsewhere: RCSB PDB 4J6E · PDBe 4J6E · UniProt B8GWR0
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