8Y57

Anti MDMA antibody 1bB11 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.248 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of an antibody specifically recognizing 3,4-methyl enedioxy methamphetamine through the epoxide moiety.

Cheon, G.Hwang, D.Le, T.C.Lee, Y.Han, E.An, S.Jung, Y.Chung, H.Lee, S.

(2024) Biochem Biophys Res Commun 733: 150607-150607

  • DOI: https://doi.org/10.1016/j.bbrc.2024.150607
  • Primary Citation of Related Structures:  
    8Y57

  • PubMed Abstract: 

    3,4-methylenedioxymethamphetamine (MDMA) or publicly known as "ecstasy" is a drug abuse substance. Since antibodies that detect MDMA typically also recognize its chemical analogue, methamphetamine (METH), we identified antibodies specifically recognizing MDMA, but not METH, named 1bB11 and 1bF12, using phage display. The crystal structure of 1bB11 in complex with MDMA was determined at 3.2 Å resolution. Key interactions were found between the epoxide moiety of MDMA and S34 and Y36 of the light chain. Additional interaction with E33 of the heavy chain contributes to anchoring MDMA. Mutagenesis-based biochemical analysis confirmed the importance of these residues in MDMA binding. Comparing the structure of 1bB11 to a scFv6H4, which binds both METH and MDMA, revealed opposite binding orientations. Taken together, our data provides a structural framework for selective binding to MDMA by the 1bB11 antibody, paving a way to develop a highly specific antibody for diagnosis.


  • Organizational Affiliation

    Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 1bB11A [auth C],
C [auth A]
233synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 1bB11B [auth D],
D [auth B]
221synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B41 (Subject of Investigation/LOI)
Query on B41

Download Ideal Coordinates CCD File 
E [auth B](2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine
C11 H15 N O2
SHXWCVYOXRDMCX-QMMMGPOBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.248 
  • Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.12α = 90
b = 254.12β = 90
c = 254.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2017R1A5A1014560
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-00223552
National Research Foundation (NRF, Korea)Korea, Republic Of2021M3A9I4022936
National Research Foundation (NRF, Korea)Korea, Republic Of2020M3A9E4038938
National Research Foundation (NRF, Korea)Korea, Republic Of2022R1A2C100988211

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references