3PS1

Crystal structure of the Escherichia Coli LPXC/LPC-011 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 3PS1

Classification: HYDROLASE / ANTIBIOTIC

Total Structure Weight: 34431.59

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase A 300 Escherichia coli EC#: 3.5.1 IUBMB
Fragment: UNP residues 1-300
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZH2
Query on ZH2

A 4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N- [(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan- 2-yl]benzamide
C21 H19 N3 O4
SNVYDNOGPYZQEV-KUHUBIRLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UKW
Query on UKW

A 4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide
C13 H12 N2 O4
JJXZDQZGPLQGCP-KCJUWKMLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ZH2 N/A in BindingDB
N/A in BindingMoad
Ki: 0.067 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.193
  • Space Group: P 61

Unit Cell:

Length (Å) Angle (°)
a = 107.13 α = 90.00
b = 107.13 β = 90.00
c = 52.09 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-11-30
  • Released Date: 2011-01-19
  • Deposition author(s): Lee, C.-J, Zhou, P.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2015-09-23
    Type: Non-polymer description