1A0Q

29G11 COMPLEXED WITH PHENYL [1-(1-N-SUCCINYLAMINO)PENTYL] PHOSPHONATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A comparison of the crystallographic structures of two catalytic antibodies with esterase activity.

Buchbinder, J.L.Stephenson, R.C.Scanlan, T.S.Fletterick, R.J.

(1998) J.Mol.Biol. 282: 1033-1041

  • DOI: 10.1006/jmbi.1998.2025

  • PubMed Abstract: 
  • The crystallographic structure of the Fab fragment of the catalytic antibody, 29G11, complexed with an (S)-norleucine phenyl phosphonate transition state analog was determined at 2.2 A resolution. The antibody catalyzes the hydrolysis of norleucine p ...

    The crystallographic structure of the Fab fragment of the catalytic antibody, 29G11, complexed with an (S)-norleucine phenyl phosphonate transition state analog was determined at 2.2 A resolution. The antibody catalyzes the hydrolysis of norleucine phenyl ester with (S)-enantioselectivity. The shape and charge complementarity of the binding pocket for the hapten account for the preferential binding of the (S)-enantiomer of the substrate. The structure is compared to that of the more catalytically efficient antibody, 17E8, induced by the same hapten transition state analog. 29G11 has different residues from 17E8 at eight positions in the heavy chain, including four substitutions in the hapten-binding pocket: A33V, S95G, S99R and Y100AN, and four substitutions at positions remote from the catalytic site, I28T, R40K, V65G and F91L. The two antibodies show large differences in the orientations of their variable and constant domains, reflected by a 32 degrees difference in their elbow angles. The VL and VH domains in the two antibodies differ by a rotation of 8.8 degrees. The hapten binds in similar orientations and locations in 29G11 and 17E8, which appear to have catalytic groups in common, though the changes in the association of the variable domains affect the precise positioning of residues in the hapten-binding pocket.


    Related Citations: 
    • Crystal Structure of a Catalytic Antibody with a Serine Protease Active Site
      Zhou, G.W.,Guo, J.,Huang, W.,Fletterick, R.J.,Scanlan, T.S.
      (1994) Science 265: 1059


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
29G11 FAB (LIGHT CHAIN)
L
212Mus musculusN/A
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
29G11 FAB (HEAVY CHAIN)
H
217Mus musculusGene Names: Ighg1 (Igh-4)
Find proteins for P01869 (Mus musculus)
Go to UniProtKB:  P01869
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HEP
Query on HEP

Download SDF File 
Download CCD File 
H
PHENYL[1-(N-SUCCINYLAMINO)PENTYL]PHOSPHONATE
C15 H22 N O6 P
FJQWWGCHPFSERW-CQSZACIVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HEPKi: 27 nM BINDINGMOAD
HEPKi: 27 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.780α = 90.00
b = 82.610β = 90.00
c = 132.340γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-02
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance