Research workbench
Co-crystal structure of P. aeruginosa lpxc-50228 complex
Analyse Co-crystal structure of P. aeruginosa lpxc-50228 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MO5
- Type
- protein
- Length
- 303 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-acyl-N-acetylglucosamine deacetylase
- EC
- 3.5.1.108
- UniProt
- P47205
- Ligands
- JWP, MG
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 303 | 24% helix, 32% strand | P47205 |
Ligands and binding sites
- JWP · N-[(2S)-1-(hydroxyamino)-3-methyl-3-{[(oxetan-3-yl) methyl]sulfonyl}-1-oxobutan-2-yl]-4-(6-hydroxyhexa-1, 3-diyn-1-yl)benzamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.72 | 0.91 | 27 | empty |
| 2 | 370 | 0.68 | 0.81 | 41 | JWP |
| 3 | 56 | 0.38 | 0.80 | 16 | empty |
| 4 | 69 | 0.34 | 0.76 | 17 | empty |
Compared structures
- 6MO5 · Co-Crystal structure of P. aeruginosa LpxC-50228 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P47205 · AlphaFold monomer V2.0 prediction for udp-3-O-acyl-N- acetylglucosamine deacetylase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P47205
- Elsewhere: RCSB PDB 6MO5 · PDBe 6MO5 · UniProt P47205
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