MolNFT v1 · #100217 · protein
Crystal structure of the escherichia COLI LPXC/LPC-138 complex
4MQY · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Crystal structure of the escherichia COLI LPXC/LPC-138 complex”. X-ray diffraction, 4 ligands (2CW, UKW, ZN), 3 pockets (best druggability 0.65). MolNFT v1 #100217 on…
- PDB
- 4MQY
- Type
- protein
- Length
- 302 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
- 2CW, UKW, ZN, SO4
- Pockets
- 3 · best druggability 0.65
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 | 302 | 27% helix, 31% strand | D5CV28 |
Ligands and binding sites
- 2CW · 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-2-methyl-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 · 5 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 396 | 0.65 | 0.79 | 46 | 2CW, DMS, SO4 |
| 2 | 74 | 0.55 | 0.87 | 22 | empty |
| 3 | 68 | 0.38 | 0.79 | 17 | empty |
Compared structures
- 4MQY · Crystal Structure of the Escherichia coli LpxC/LPC-138 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 4MQY · PDBe 4MQY · UniProt D5CV28
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