Research workbench
Crystal structure of the pseudomonas aeruginosa LPXC/LPC-009 complex
Analyse Crystal structure of the pseudomonas aeruginosa LPXC/LPC-009 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P3E
- Type
- protein
- Length
- 297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.-
- UniProt
- P47205
- Ligands
- 3P3, ZN, NA, NO3
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 297 | 25% helix, 32% strand | P47205 |
Ligands and binding sites
- 3P3 · N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal
- NO3 · Nitrate ion · ion · 25 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.70 | 0.81 | 51 | 3P3, NO3 |
| 2 | 150 | 0.60 | 0.83 | 26 | NO3 |
| 3 | 55 | 0.38 | 0.81 | 18 | empty |
Compared structures
- 3P3E · Crystal Structure of the PSEUDOMONAS AERUGINOSA LpxC/LPC-009 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 0.98
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 3P3E · PDBe 3P3E · UniProt P47205
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