5ODB

Crystal structure of the RA-associated mAb D10 (chimeric Fab fragment)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies.

Ge, C.Xu, B.Liang, B.Lonnblom, E.Lundstrom, S.L.Zubarev, R.A.Ayoglu, B.Nilsson, P.Skogh, T.Kastbom, A.Malmstrom, V.Klareskog, L.Toes, R.E.M.Rispens, T.Dobritzsch, D.Holmdahl, R.

(2019) Arthritis Rheumatol 71: 210-221

  • DOI: 10.1002/art.40698
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Anti-citrullinated protein antibodies (ACPAs) develop many years before the clinical onset of rheumatoid arthritis (RA). This study was undertaken to address the molecular basis of the specificity and cross-reactivity of ACPAs from patients with RA.

    Anti-citrullinated protein antibodies (ACPAs) develop many years before the clinical onset of rheumatoid arthritis (RA). This study was undertaken to address the molecular basis of the specificity and cross-reactivity of ACPAs from patients with RA.


    Organizational Affiliation

    Karolinska Institutet, Stockholm, Sweden.,Karolinska Institutet, Stockholm, Sweden, and Southern Medical University, Guangzhou, China.,Uppsala University, Uppsala, Sweden.,KTH Royal Institute of Technology, Stockholm, Sweden.,Linköping University, Linköping, Sweden.,Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Leiden University Medical Center, Leiden, The Netherlands.,University of Amsterdam, Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D10 Fab fragment - heavy chain
A
223N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D10 Fab fragment - light chain
B
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.368α = 90.00
b = 66.714β = 93.85
c = 72.764γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
xia2data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSwedenKAW 2010.0148
Swedish Research CouncilSwedenK2011-52X-07931-25-5

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2019-08-07
    Type: Data collection, Database references