4KUC | pdb_00004kuc

Crystal structure of ricin-A chain in complex with the antibody 6C2

• PDB DOI: https://doi.org/10.2210/pdb4KUC/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Ricinus communis, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-21 Released: 2013-07-17 
• Deposition Author(s): Zhu, Y., Li, X., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 
  0.289 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Structural insights into the neutralization mechanism of mAb 6C2 against ricin

Zhu, Y., Li, X., Teng, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 161.19 kDa 
• Atom Count: 8,287 
• Modeled Residue Count: 1,156 
• Deposited Residue Count: 1,470 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ricin	A, D [auth I]	267	Ricinus communis	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P02879 (Ricinus communis) Explore P02879  Go to UniProtKB:  P02879

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb6c2 fab-Heavy chain	B [auth D], E	231	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mAb6c2 fab-Light chain	C [auth H], F	237	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free:  0.289 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.516	α = 90
b = 151.803	β = 90
c = 208.418	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Zhu, Y., Li, X., Teng, M.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary