Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52843.71 
• Atom Count: 3672 
• Residue Count: 484 
• Unique protein chains: 2

1T6V

Crystal structure analysis of the nurse shark new antigen receptor (NAR) variable domain in complex with lysozyme

• DOI: 10.2210/pdb1T6V/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Ginglymostoma cirratum, Gallus gallus
• Expression System: Escherichia coli


• Deposited: 2004-05-07 Released: 2004-08-24 
• Deposition Author(s): Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 

Literature

Crystal structure of a shark single-domain antibody V region in complex with lysozyme.

Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

(2004) Science 305: 1770-1773

• PubMed: 15319492 
• DOI: 10.1126/science.1101148
• Primary Citation of Related Structures:  
  1SQ2


• PubMed Abstract: 
  

Cartilaginous fish are the phylogenetically oldest living organisms known to possess components of the vertebrate adaptive immune system. Key to their immune response are heavy-chain, homodimeric immunoglobulins called new antigen receptors (IgNARs), in which the variable (V) domains recognize antigens with only a single immunoglobulin domain, akin to camelid heavy-chain V domains. The 1.45 angstrom resolution crystal structure of the type I IgNAR V domain in complex with hen egg-white lysozyme (HEL) reveals a minimal antigen-binding domain that contains only two of the three conventional complementarity-determining regions but still binds HEL with nanomolar affinity by means of a binding interface comparable in size to conventional antibodies.

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Organizational Affiliation: 

Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme C	L, M	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Go to Gene View: LYZ Go to UniProtKB:  P00698

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
novel antigen receptor	N, O	113	Ginglymostoma cirratum	Mutation(s): 0
Find proteins for Q8AXI4 (Ginglymostoma cirratum) Go to UniProtKB:  Q8AXI4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	N, O	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.221 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 75.790	α = 90.00
b = 113.810	β = 90.00
c = 58.440	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
EPMR	phasing
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-07 
• Released Date: 2004-08-24 
• Deposition Author(s): Stanfield, R.L., Dooley, H., Flajnik, M.F., Wilson, I.A.

Revision History 

• Version 1.0: 2004-08-24
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance