MolNFT v1 · #75497 · protein
Crystal structure of the escherichia COLI LPXC/LPC-012 complex
3PS2 · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Crystal structure of the escherichia COLI LPXC/LPC-012 complex”. X-ray diffraction, 4 ligands (ZH4, UKW, ZN), 2 pockets (best druggability 0.62). MolNFT v1 #75497 on…
- PDB
- 3PS2
- Type
- protein
- Length
- 300 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
- D5CV28
- Ligands
- ZH4, UKW, ZN, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 300 | 27% helix, 31% strand | D5CV28 |
Ligands and binding sites
- ZH4 · 4-[4-(3-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-nitroso-1-oxobutan-2-yl]benzamide · ligand · chains A
- UKW · 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.62 | 0.77 | 45 | ZH4, DMS, SO4 |
| 2 | 61 | 0.38 | 0.79 | 16 | empty |
Compared structures
- 3PS2 · Crystal structure of the Escherichia Coli LPXC/LPC-012 complex · the same entry in another collection · chain A against A, TM-score 1.00
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 D5CV28
- Elsewhere: RCSB PDB 3PS2 · PDBe 3PS2 · UniProt D5CV28
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