5K8K

Structure of the Haemophilus influenzae LpxH-lipid X complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 5K8K

Classification: HYDROLASE

Total Structure Weight: 31639.98

Macromolecule Entities
Molecule Chains Length Organism Details
UDP-2,3-diacylglucosamine hydrolase A 256 Haemophilus influenzae EC#: 3.6.1.54 IUBMB
Gene Name(s): lpxH HI_0735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LP5
Query on LP5

A (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)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-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
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.192
  • Space Group: H 3 2

Unit Cell:

Length (Å) Angle (°)
a = 99.84 α = 90.00
b = 99.84 β = 90.00
c = 200.85 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-05-30
  • Released Date: 2016-08-10
  • Deposition author(s): Cho, J., Lee, C.-J., Zhou, P.

Revision History

  • Version 1_0: 2016-08-10

    Type: Initial release

  • Version 1_1: 2016-09-21

    Type: Database references

  • Version 1_2: 2016-11-09

    Type: Database references

  • Version 1_3: 2017-09-20

    Type: Author supporting evidence, Derived calculations