1MJJ

HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION-STATE ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report



Literature

High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity

Ruzheinikov, S.N.Muranova, T.A.Sedelnikova, S.E.Partridge, L.J.Blackburn, G.M.Murray, I.A.Kakinuma, H.Takashi, N.Shimazaki, K.Sun, J.Nishi, Y.Rice, D.W.

(2003) J Mol Biol 332: 423-435

  • DOI: 10.1016/s0022-2836(03)00902-1
  • Primary Citation of Related Structures:  
    1MH5, 1MIE, 1MJJ, 1MJ8, 1MJ7, 1MJU

  • PubMed Abstract: 
  • The crystal structures of four related Fab fragments of a family of catalytic antibodies displaying differential levels of esterase activity have been solved in the presence and in the absence of the transition-state analogue (TSA) that was used to e ...

    The crystal structures of four related Fab fragments of a family of catalytic antibodies displaying differential levels of esterase activity have been solved in the presence and in the absence of the transition-state analogue (TSA) that was used to elicit the immune response. The electron density maps show that the TSA conformation is essentially identical, with limited changes on hapten binding. Interactions with the TSA explain the specificity for the D rather than the L-isomer of the substrate. Differences in the residues in the hapten-binding pocket, which increase hydrophobicity, appear to correlate with an increase in the affinity of the antibodies for their substrate. Analysis of the structures at the active site reveals a network of conserved hydrogen bond contacts between the TSA and the antibodies, and points to a critical role of two conserved residues, HisL91 and LysH95, in catalysis. However, these two key residues are set into very different contexts in their respective structures, with an apparent direct correlation between the catalytic power of the antibodies and the complexity of their interactions with the rest of the protein. This suggests that the catalytic efficiency may be controlled by contacts arising from a second sphere of residues at the periphery of the active site.


    Related Citations: 
    • The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue
      Muranova, T.A., Ruzheinikov, S.N., Sedelnikova, S.E., Moir, A., Partridge, L.J., Kakinuma, H., Takashi, N., Shimazaki, K., Sun, J., Nishi, Y., Rice, D.W.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1192

    Organizational Affiliation

    Krebs Institute for Biomolecular Research, University of Sheffield, Firth Court, Western Bank, S10 2TN Sheffield, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN MS6-12A, L219Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN MS6-12B, H227Mus musculusMutation(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
HAL
Query on HAL

Download CCD File 
A, H
N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
C23 H29 N2 O7 P
DKQZZKSBRCTCQU-QFIPXVFZSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B,HL-PEPTIDE LINKINGC5 H7 N O3GLN
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HALKd:  1.8300000429153442   nM  Binding MOAD
HALKd :  1.8300000429153442   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.281α = 90
b = 93.841β = 90
c = 142.798γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Derived calculations, Polymer sequence