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Crystal structure of P.aeruginosa LpxC in complex with inhibitor
Analyse Crystal structure of P.aeruginosa LpxC in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DEN
- Type
- protein
- Length
- 295 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.07
- Source
- Pseudomonas aeruginosa PAO1
- Molecule
- UDP-3-O-acyl-N-acetylglucosamine deacetylase
- EC
- 3.5.1.108
- UniProt
- P47205
- Ligands
- H4R, ZN
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.07 · 1 distinct chain · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UDP-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 295 | 25% helix, 33% strand | P47205 |
Ligands and binding sites
- H4R · 4-[(1~{R},5~{S})-6-[2-[4-[3-[[2-[(1~{S})-1-oxidanylethyl]imidazol-1-yl]methyl]-1,2-oxazol-5-yl]phenyl]ethynyl]-3-azabicyclo[3.1.0]hexan-3-yl]butanoic acid · ligand · chains A
- ZN · Zinc 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 | 389 | 0.70 | 0.82 | 42 | ZN, H4R |
| 2 | 179 | 0.67 | 0.86 | 29 | empty |
| 3 | 67 | 0.43 | 0.82 | 18 | empty |
| 4 | 56 | 0.29 | 0.75 | 14 | empty |
Compared structures
- 7DEN · Crystal structure of P.AERUGINOSA lpxc in complex with inhibitor · 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 0.99
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 7DEN · PDBe 7DEN · UniProt P47205
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