1MJ7

Crystal Structure Of The Complex Of The Fab fragment of Esterolytic Antibody MS5-393 and A Transition-State Analog

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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 elicit the immune response ...

    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 MS5-393A [auth L]219Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN MS5-393B [auth H]228Mus musculusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAL (Subject of Investigation/LOI)
Query on HAL
Download Ideal Coordinates CCD File 
 C [auth H]N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
C23 H29 N2 O7 P
DKQZZKSBRCTCQU-QFIPXVFZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HAL PDBBind:  1MJ7 Kd: 4.5 (nM) from 1 assay(s)
Binding MOAD:  1MJ7 Kd: 4.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.237α = 90
b = 40.531β = 109.72
c = 85.903γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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 1.3: 2011-11-16
    Changes: Atomic model