1C5C | pdb_00001c5c

DECARBOXYLASE CATALYTIC ANTIBODY 21D8-HAPTEN COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1C5C/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-09 Released: 2000-10-11 
• Deposition Author(s): Hotta, K., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.196 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Models: experimental

Literature

Catalysis of decarboxylation by a preorganized heterogeneous microenvironment: crystal structures of abzyme 21D8.

Hotta, K., Lange, H., Tantillo, D.J., Houk, K.N., Hilvert, D., Wilson, I.A.

(2000) J Mol Biology 302: 1213-1225

• PubMed: 11183784 
• DOI: https://doi.org/10.1006/jmbi.2000.4503
• Primary Citation Related Structures: 
  1C5B, 1C5C


• PubMed Abstract: 
  

  Antibody 21D8 catalyzes the solvent-sensitive decarboxylation of 3-carboxybenzisoxazoles. The crystal structure of chimeric Fab 21D8 with and without hapten at 1.61 A and 2.10 A, respectively, together with computational analysis, shows how a melange of polar and non-polar sites are exploited to achieve both substrate binding and acceleration of a reaction normally facilitated by purely aprotic dipolar media. The striking similarity of the decarboxylase and a series of unrelated esterase antibodies also highlights the chemical versatility of structurally conserved anion binding sites and the relatively subtle changes involved in fine-tuning the immunoglobulin pocket for recognition of different ligands and catalysis of different reactions.

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Organizational Affiliation: 
• Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 47.05 kDa 
• Atom Count: 3,642 
• Modeled Residue Count: 429 
• Deposited Residue Count: 429 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIMERIC DECARBOXYLASE ANTIBODY 21D8	A [auth L]	214	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CHIMERIC DECARBOXYLASE ANTIBODY 21D8	B [auth H]	215	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TK4	C [auth L]	2-ACETYLAMINO-NAPTHALENE-1,5-DISULFONIC ACID C12 H11 N O7 S2 WGOQGHNONXFNJQ-UHFFFAOYSA-N
GOL	D [auth H], E [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.253 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.196 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.217	α = 90
b = 43.932	β = 90
c = 221.205	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MERLOT	phasing
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-11 
Deposition Author(s): Hotta, K., Wilson, I.A.

Revision History  

• Version 1.0: 2000-10-11
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary