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 
  • R-Value Observed: 0.189 

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
  • Structures With Same Primary Citation

  • 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.


    Organizational Affiliation

    Karolinska Institutet, Stockholm, Sweden, and Southern Medical University, Guangzhou, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D10 Fab fragment - heavy chainA223Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D10 Fab fragment - light chainB213Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download CCD File 
B
GLYCEROL
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 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.368α = 90
b = 66.714β = 93.85
c = 72.764γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Data collection, Database references