1C1E | pdb_00001c1e

CRYSTAL STRUCTURE OF A DIELS-ALDERASE CATALYTIC ANTIBODY 1E9 IN COMPLEX WITH ITS HAPTEN

• PDB DOI: https://doi.org/10.2210/pdb1C1E/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1999-07-22 Released: 2000-03-01 
• Deposition Author(s): Xu, J., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.294 (Depositor) 
• R-Value Work: 
  0.239 (Depositor) 
• R-Value Observed: 
  0.250 (Depositor) 

Literature

Evolution of shape complementarity and catalytic efficiency from a primordial antibody template.

Xu, J., Deng, Q., Chen, J., Houk, K.N., Bartek, J., Hilvert, D., Wilson, I.A.

(1999) Science 286: 2345-2348

• PubMed: 10600746 
• DOI: https://doi.org/10.1126/science.286.5448.2345
• Primary Citation of Related Structures:  
  1C1E


• PubMed Abstract: 
  

  The crystal structure of an efficient Diels-Alder antibody catalyst at 1.9 angstrom resolution reveals almost perfect shape complementarity with its transition state analog. Comparison with highly related progesterone and Diels-Alderase antibodies that arose from the same primordial germ line template shows the relatively subtle mutational steps that were able to evolve both structural complementarity and catalytic efficiency.

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Organizational Affiliation: 
• Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.01 kDa 
• Atom Count: 3,563 
• Modeled Residue Count: 435 
• Deposited Residue Count: 435 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALYTIC ANTIBODY 1E9 (LIGHT CHAIN)	A [auth L]	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALYTIC ANTIBODY 1E9 (HEAVY CHAIN)	B [auth H]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ENH	D [auth H]	1,7,8,9,10,10-HEXACHLORO-4-METHYL-4-AZA-TRICYCLO[5.2.1.0(2,6)]DEC-8-ENE-3,5-DIONE C10 H5 Cl6 N O2 DKILHSLDAKXHHE-ASQNABRVSA-N
MLT	C [auth L]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.294 (Depositor) 
• R-Value Work:  0.239 (Depositor) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.73	α = 90
b = 132.44	β = 90
c = 167.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-01 
Deposition Author(s): Xu, J., Wilson, I.A.

Revision History  

• Version 1.0: 2000-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-01-30
  Changes: Non-polymer description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary