5DQD

Structure of S55-5 Fab in complex with lipid A carbohydrate backbone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 5DQD

Classification: IMMUNE SYSTEM

Total Structure Weight: 48589.64

Macromolecule Entities
Molecule Chains Length Organism Details
S55-5 Fab (IgG1 kappa) light chain L 218 Mus musculus
S55-5 Fab (IgG1) heavy chain H 222 Mus musculus

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KD2
Query on KD2

H 2-(acetylamino)-6-O-[2-(acetylamino)-2-deoxy- 4-O-phosphono-beta-D-glucopyranosyl]-2-deoxy- 1-O-phosphono-alpha-D-glucopyranose
C16 H30 N2 O17 P2
UBTXJJWURAYTBU-MVGRPQHISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.172
  • Space Group: P 2 21 21

Unit Cell:

Length (Å) Angle (°)
a = 56.38 α = 90.00
b = 64.79 β = 90.00
c = 129.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-09-14
  • Released Date: 2016-03-09
  • Deposition author(s): Haji-Ghassemi, O., Evans, S.V.

Revision History

  • Version 1_0: 2016-03-09

    Type: Initial release