Research workbench
Pseudomonas aeruginosa lpxc in complex with nvs-lpxc-01
Analyse Pseudomonas aeruginosa lpxc in complex with nvs-lpxc-01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U3B
- Type
- protein
- Length
- 591 residues
- Chains
- 2
- 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
- 7TD, ZN
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 297 | 24% helix, 34% strand | P47205 |
| B | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 294 | 25% helix, 34% strand | P47205 |
Ligands and binding sites
- 7TD · N-[(2S)-3-amino-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]-4-[(but-2-yn-1-yl)oxy]benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.69 | 0.90 | 19 | empty |
| 2 | 138 | 0.67 | 0.88 | 25 | empty |
| 3 | 351 | 0.66 | 0.80 | 41 | 7TD |
| 4 | 364 | 0.66 | 0.80 | 44 | ZN, 7TD |
| 5 | 625 | 0.66 | 0.76 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 110 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U3B · Pseudomonas aeruginosa LpxC in complex with NVS-LPXC-01 · 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 5U3B · PDBe 5U3B · UniProt P47205
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