Research workbench
Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor
Analyse Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VWM
- Type
- protein
- Length
- 300 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847…
- Molecule
- UDP-3-O-acyl-N-acetylglucosamine deacetylase
- EC
- 3.5.1.108
- UniProt
- P47205
- Ligands
- C90, ZN, CA, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 24% 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 | 300 | 24% helix, 33% strand | P47205 |
Ligands and binding sites
- C90 · N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 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 | 165 | 0.67 | 0.86 | 27 | empty |
| 2 | 331 | 0.64 | 0.80 | 41 | C90, CL |
| 3 | 56 | 0.39 | 0.81 | 18 | empty |
Compared structures
- 5VWM · Crystal structure of udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (lpxc)… · 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 5VWM · PDBe 5VWM · UniProt P47205
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.