Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

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

Macromolecule Content

• Total Structure Weight: 47.73 kDa 
• Atom Count: 3359 
• Residue Count: 435 
• Unique protein chains: 2

1DBA

THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX

• DOI: 10.2210/pdb1DBA/pdb

• Classification: IMMUNOGLOBULIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 1992-11-10 Released: 1993-10-31 
• Deposition Author(s): Arevalo, J.H., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex.

Arevalo, J.H., Stura, E.A., Taussig, M.J., Wilson, I.A.

(1993) J Mol Biol 231: 103-118

• PubMed: 8496956 
• DOI: 10.1006/jmbi.1993.1260
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.

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Related Citations: 

• Analysis of an Anti-Progesterone Antibody: Variable Crystal Morphology of the Fab' and Steroid-Fab' Complexes
  Stura, E.A., Arevalo, J.H., Feinstein, A., Heap, R.B., Taussig, M.J., Wilson, I.A.
  (1987) Immunology 62: 511

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Organizational Affiliation: 

Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
IGG1-KAPPA DB3 FAB (LIGHT CHAIN)	L	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
IGG1-KAPPA DB3 FAB (HEAVY CHAIN)	H	219	Mus musculus	Mutation(s): 0  Gene Names: Ighg1, Igh-4
Find proteins for P01868 (Mus musculus) Explore P01868  Go to UniProtKB:  P01868

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	H	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.76	α = 90
b = 134.76	β = 90
c = 124.21	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1992-11-10 
• Released Date: 1993-10-31 
Deposition Author(s): Arevalo, J.H., Wilson, I.A.

Revision History 

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance