1SBS | pdb_00001sbs

CRYSTAL STRUCTURE OF AN ANTI-HCG FAB

• PDB DOI: https://doi.org/10.2210/pdb1SBS/pdb

• Classification: MONOCLONAL ANTIBODY
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1998-04-08 Released: 1999-04-13 
• Deposition Author(s): Fotinou, C., Beauchamp, J., Emsley, P., Dehaan, A., Schielen, W.J.G., Bos, E., Isaacs, N.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.180 (Depositor) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of an Fab fragment against a C-terminal peptide of hCG at 2.0 A resolution.

Fotinou, C., Beauchamp, J., Emsley, P., deHaan, A., Schielen, W.J., Bos, E., Isaacs, N.W.

(1998) J Biological Chem 273: 22515-22518

• PubMed: 9712877 
• DOI: https://doi.org/10.1074/jbc.273.35.22515
• Primary Citation Related Structures: 
  1SBS


• PubMed Abstract: 
  

  3A2 is an antibody raised against human chorionic gonadotropin and recognizes a linear epitope on the C-terminal peptide of the human chorionic gonadotropin beta-subunit. Its three-dimensional structure has been determined to 2-A resolution using molecular replacement and refined to a conventional R-factor of 18.2%. The protein exhibits the typical immunoglobulin fold, and the model contains 944 ordered water molecules and one sulfate ion. A comparison of the complementarity-determining regions of the Fab3A2 with those from the Protein Data Bank following the canonical structure method reveals a canonical main chain conformation. This antibody belongs to the canonical structure class (combination of canonical conformations of the complementarity determining loops) that shows a preference for haptens and not for peptides. However, the shape of the surface of the antigen binding loops resembles that of an anti-peptide antibody.

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Organizational Affiliation: 
• Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.66 kDa 
• Atom Count: 4,360 
• Modeled Residue Count: 442 
• Deposited Residue Count: 442 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 3A2	A [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MONOCLONAL ANTIBODY 3A2	B [auth L]	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.180 (Depositor) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.8	α = 90
b = 74.8	β = 90
c = 198.205	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
ROTAVATA/AGROVATA	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-13 
Deposition Author(s): Fotinou, C., Beauchamp, J., Emsley, P., Dehaan, A., Schielen, W.J.G., Bos, E., Isaacs, N.W.

Revision History  

• Version 1.0: 1999-04-13
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary