Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 49015.73 
• Atom Count: 3351 
• Residue Count: 441 
• Unique protein chains: 2

3BPC

co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo

• DOI: 10.2210/pdb3BPC/pdb

• Classification: IMMUNE SYSTEM


• Deposited: 2007-12-18 Released: 2009-01-13 
• Deposition Author(s): Brooks, C.L., Evans, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 

Literature

Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.

Brooks, C.L., Muller-Loennies, S., Brade, L., Kosma, P., Hirama, T., MacKenzie, C.R., Brade, H., Evans, S.V.

(2008) J.Mol.Biol. 377: 450-468

• PubMed: 18272175 
• DOI: 10.1016/j.jmb.2008.01.018
• Primary Citation of Related Structures:  
  2R2H, 2R2E, 2R2B, 2R23, 2R1X, 2R1Y, 2R1W


• PubMed Abstract: 
  

To explore the molecular basis of antigen recognition by germline antibodies, we have determined to high resolution the structures of the near-germline monoclonal antibody S25-2 in complex with seven distinct carbohydrate antigens based on the bacterial sugar 3-deoxy-alpha-D-manno-oct-2-ulosonic acid (Kdo). In contrast to previous findings, the inherited germline Kdo monosaccharide binding site is not restricted to this bacterial sugar but is able to accommodate an array of substitutions and chemical modifications of Kdo, including naturally occurring antigens containing the related monosaccharide d-glycero-alpha-d-talo-oct-2-ulosonic acid as well as nonterminal Kdo residues. However, we show by surface plasmon resonance and ELISA how antibody S25-2 specificity is so dependent on the context in which the antigen is presented that a free disaccharide displays strong binding while the same lipid-A-bound disaccharide does not bind. These structures provide insight into how inherited germline genes code for immunoglobulins of limited flexibility that are capable of binding a range of epitopes from which affinity-matured antibodies are generated.

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Organizational Affiliation: 

Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Fab, antibody fragment (IgG1k), light chain	A	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Fab, antibody fragment (IgG1k), heavy chain	B	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
KDA	B	(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL C11 H18 O8 LEEKAQBTVJRLOA-UEWQFTGXSA-N
KDB	A	3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid 3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid C8 H12 O6 ITFIFEKDEVIBCW-GKROBHDKSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
KDA	Kd: 16000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.273 
• R-Value Work: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 45.850	α = 90.00
b = 81.290	β = 90.00
c = 132.340	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-12-18 
• Released Date: 2009-01-13 
• Deposition Author(s): Brooks, C.L., Evans, S.V.

Revision History 

• Version 1.0: 2009-01-13
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2018-03-07
  Type: Data collection