4KUZ

Crystal structure of anti-emmprin antibody 4A5 Fab in trigonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural evidence for a constrained conformation of short CDR-L3 in antibodies.

Teplyakov, A.Obmolova, G.Malia, T.J.Luo, J.Gilliland, G.L.

(2014) Proteins 82: 1679-1683

  • DOI: 10.1002/prot.24522
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Three Fab structures used as targets in the Antibody Modeling Assessment presented a challenge for modeling CDR-L3 due to deviations from the most typical canonical structure. In all three antibodies CDR-L3 has eight residues, which is one residue sh ...

    Three Fab structures used as targets in the Antibody Modeling Assessment presented a challenge for modeling CDR-L3 due to deviations from the most typical canonical structure. In all three antibodies CDR-L3 has eight residues, which is one residue shorter than usual, and has a conformation that is rarely observed in crystal structures. We analyzed the sequence and structural determinants of this conformation and found that the "short" CDR-L3 is remarkably rigid and retains the conformation in the interactions with antigens and neighboring CDRs.


    Organizational Affiliation

    Janssen Research & Development, LLC, Spring House, Pennsylvania, 19477.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
antibody 4A5 light chain
L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
antibody 4A5 heavy chain
H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
H, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.230 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.430α = 90.00
b = 126.430β = 90.00
c = 97.150γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CrystalCleardata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references