MolNFT v1 · #73357 · protein
Structure of lpxc from yersinia enterocolitica complexed with CHIR090 inhibitor
3NZK · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “Structure of lpxc from yersinia enterocolitica complexed with CHIR090 inhibitor”. X-ray diffraction, 2 ligands (C90, ZN), 4 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3NZK
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
- EC
- 3.5.1.33
- UniProt
- A1JJJ9
- Ligands
- C90, ZN
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.33) | protein | 298 | 26% helix, 31% strand | A1JJJ9 |
| B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.33) | protein | 300 | 26% helix, 31% strand | A1JJJ9 |
Ligands and binding sites
- C90 · N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.72 | 0.76 | 77 | empty |
| 2 | 437 | 0.69 | 0.80 | 43 | C90 |
| 3 | 410 | 0.69 | 0.80 | 42 | C90 |
| 4 | 62 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 284 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3NZK · Structure of LpxC from Yersinia enterocolitica Complexed with CHIR090 Inhibitor · 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 A1JJJ9
- Elsewhere: RCSB PDB 3NZK · PDBe 3NZK · UniProt A1JJJ9
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