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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from unrelated V-genes

Haji-Ghassemi, O.Muller-Loennies, S.Rodriguez, T.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2015) J.Biol.Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S55-5 Fab (IgG1 kappa) light chain
L
218N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S55-5 Fab (IgG1) heavy chain
H
222N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
KD2
Query on KD2

Download SDF File 
Download CCD File 
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 Interaction
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 = 56.385α = 90.00
b = 64.793β = 90.00
c = 129.771γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release