1NGX

Chimeric Germline Fab 7g12 with jeffamine fragment bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 

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This is version 1.3 of the entry. See complete history


Literature

Structural evidence for substrate strain in antibody catalysis

Yin, J.Andryski, S.E.Beuscher, A.B.Stevens, R.C.Schultz, P.G.

(2003) Proc Natl Acad Sci U S A 100: 856-861

  • DOI: https://doi.org/10.1073/pnas.0235873100
  • Primary Citation of Related Structures:  
    1N7M, 1NGW, 1NGX, 1NGY, 1NGZ

  • PubMed Abstract: 

    The crystal structure of the Michaelis complex between the Fab fragment of ferrochelatase antibody 7G12 and its substrate mesoporphyrin has been solved to 2.6-A resolution. The antibody-bound mesoporphyrin clearly adopts a nonplanar conformation and reveals that the antibody catalyzes the porphyrin metallation reaction by straining/distorting the bound substrate toward the transition-state configuration. The crystal structures of the Fab fragment of the germ-line precursor antibody to 7G12 and its complex with the hapten N-methylmesoporphyrin have also been solved. A comparison of these structures with the corresponding structures of the affinity-matured antibody 7G12 reveals the molecular mechanism by which the immune system evolves binding energy to catalyze this reaction.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Germline Metal Chelatase Catalytic Antibody, Light chainA,
C [auth L]
213Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Germline Metal Chelatase Catalytic Antibody, Heavy chainB,
D [auth H]
216Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JEF
Query on JEF

Download Ideal Coordinates CCD File 
E [auth B],
F [auth H]
O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500)
C30 H63 N O10
ICCXIDTYQFYPNV-RUMGZKRTSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.666α = 90
b = 64.723β = 92.58
c = 93.382γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation