MolNFT v1 · #46424 · protein
X-ray crystal structure of lpxc complexed with 3-heptyloxybenzoate
2O3Z · Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase: “X-ray crystal structure of lpxc complexed with 3-heptyloxybenzoate”. X-ray diffraction, 4 ligands (AI7, ZN, SO4), 2 pockets (best druggability 0.82). MolNFT v1 #46424 on…
- PDB
- 2O3Z
- Type
- protein
- Length
- 534 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.-
- UniProt
- O67648
- Ligands
- AI7, ZN, SO4, CL
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) | protein | 267 | 23% helix, 35% strand | O67648 |
Ligands and binding sites
- AI7 · 3-(heptyloxy)benzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 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 | 1175 | 0.82 | 0.83 | 109 | SO4, AI7 |
| 2 | 56 | 0.35 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 539 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2O3Z · X-ray crystal structure of LpxC complexed with 3-heptyloxybenzoate · the same entry in another collection · chain B against B, TM-score 1.00
- O67648 · 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 O67648
- Elsewhere: RCSB PDB 2O3Z · PDBe 2O3Z · UniProt O67648
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