4GGM

Structure of LpxI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 4GGM

Classification: HYDROLASE

Total Structure Weight: 31113.07

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-2,3-diacylglucosamine pyrophosphatase LpxI X 283 Caulobacter vibrioides EC#: 3.6.1.54 IUBMB
Gene Name(s): lpxI CCNA_01987
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Hydrolases

Protein Name: LpxI phosphodiester hydrolase for lipid A biosynthesis


Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LP5
Query on LP5

X (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)- 5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO- 2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
C34 H66 N O12 P
HEHQDWUWJVPREQ-XQJZMFRCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

X MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
X L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.272
  • R-Value Work: 0.216
  • Space Group: I 41 2 2

Unit Cell:

Length (Å) Angle (°)
a = 74.29 α = 90.00
b = 74.29 β = 90.00
c = 364.64 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-06
  • Released Date: 2012-10-03
  • Deposition author(s): Metzger IV, L.E., Lee, J.K., Finer-Moore, J.S., Raetz, C.R.H., Stroud, R.M., Center for Structures of Membrane Proteins (CSMP)

Revision History

  • Version 1_0: 2012-10-03

    Type: Initial release

  • Version 1_1: 2012-11-14

    Type: Database references

  • Version 1_2: 2012-11-21

    Type: Database references

  • Version 1_3: 2013-04-17

    Type: Structure summary

  • Version 1_4: 2017-10-25

    Type: Author supporting evidence