Research workbench
Chain a. udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase pa-lpxc complexed with (R)-3-((S)-3-(4-(CYCLOPROPYLETHYNYL)PHENYL)-2- oxooxazolidin-5-yl)-N-hydroxy-2-methyl-2-(METHYLSULFONYL)PROPENAMIDE
Analyse Chain a. udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase pa-lpxc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MAE
- Type
- protein
- Length
- 297 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
- JBA, ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-acyl-N-acetylglucosamine deacetylase (EC 3.5.1.108) | protein | 297 | 26% helix, 35% strand | P47205 |
Ligands and binding sites
- JBA · (2R)-3-{(5S)-3-[4-(cyclopropylethynyl)phenyl]-2-oxo-1, 3-oxazolidin-5-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)propanamide · 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 | 392 | 0.71 | 0.82 | 44 | JBA, ZN |
| 2 | 133 | 0.67 | 0.88 | 22 | empty |
| 3 | 65 | 0.46 | 0.83 | 19 | empty |
| 4 | 56 | 0.28 | 0.74 | 14 | empty |
Compared structures
- 6MAE · CHAIN A. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase PA-LPXC Complexed… · 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 6MAE · PDBe 6MAE · UniProt P47205
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