1MH5

The Structure Of The Complex Of The Fab Fragment Of The Esterolytic Antibody MS6-164 and A Transition-State Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


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

  • Primary Citation of Related Structures:  1MIE, 1MJ7, 1MJ8, 1MJJ, 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.,Sect.D 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN MS6-164
A, L
219Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IMMUNOGLOBULIN MS6-164
B, H
230Mus musculusGene Names: Ighg
Find proteins for P01863 (Mus musculus)
Go to UniProtKB:  P01863
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAL
Query on HAL

Download SDF File 
Download CCD File 
B, 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 SDF File 
Download CCD File 
B, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HALKd: 0.61 nM BINDINGMOAD
HALKd: 0.61 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.346α = 90.00
b = 117.104β = 90.14
c = 114.645γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model