2AGJ

Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 2AGJ

Classification: IMMUNE SYSTEM

Total Structure Weight: 48367.99

Macromolecule Entities
Molecule Chains Length Organism Details
Yvo Fab, Light Chain L 215 Homo sapiens Gene Name(s): IGK@
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Yvo Fab, Heavy Chain H 226 Homo sapiens Gene Name(s): IGHM
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

H N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.219
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 82.43 α = 90.00
b = 103.65 β = 90.00
c = 138.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-07-27
  • Released Date: 2006-05-02
  • Deposition author(s): Ramsland, P.A., Terzyan, S.S., Cloud, G., Bourne, C.R., Farrugia, W., Tribbick, G., Geysen, H.M., Moomaw, C.R., Slaughter, C.A., Edmundson, A.B.

Revision History

  • Version 1_0: 2006-05-02

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description