7DC7 | pdb_00007dc7

Crystal structure of D12 Fab-ATP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Exploitation of Elevated Extracellular ATP to Specifically Direct Antibody to Tumor Microenvironment.

Mimoto, F.Tatsumi, K.Shimizu, S.Kadono, S.Haraya, K.Nagayasu, M.Suzuki, Y.Fujii, E.Kamimura, M.Hayasaka, A.Kawauchi, H.Ohara, K.Matsushita, M.Baba, T.Susumu, H.Sakashita, T.Muraoka, T.Aso, K.Katada, H.Tanaka, E.Nakagawa, K.Hasegawa, M.Ayabe, M.Yamamoto, T.Tanba, S.Ishiguro, T.Kamikawa, T.Nambu, T.Kibayashi, T.Azuma, Y.Tomii, Y.Kato, A.Ozeki, K.Murao, N.Endo, M.Kikuta, J.Kamata-Sakurai, M.Ishii, M.Hattori, K.Igawa, T.

(2020) Cell Rep 33: 108542-108542

  • DOI: https://doi.org/10.1016/j.celrep.2020.108542
  • Primary Citation Related Structures: 
    7DC7, 7DC8

  • PubMed Abstract: 

    The extracellular adenosine triphosphate (ATP) concentration is highly elevated in the tumor microenvironment (TME) and remains tightly regulated in normal tissues. Using phage display technology, we establish a method to identify an antibody that can bind to an antigen only in the presence of ATP. Crystallography analysis reveals that ATP bound in between the antibody-antigen interface serves as a switch for antigen binding. In a transgenic mouse model overexpressing the antigen systemically, the ATP switch antibody binds to the antigen in tumors with minimal binding in normal tissues and plasma and inhibits tumor growth. Thus, we demonstrate that elevated extracellular ATP concentration can be exploited to specifically target the TME, giving therapeutic antibodies the ability to overcome on-target off-tumor toxicity.


  • Organizational Affiliation
    • Chugai Pharmabody Research Pte. Ltd., 3 Biopolis Drive, #07 - 11 to 16, Synapse, 138623, Singapore. Electronic address: mimoto-f@chugai-pharmabody.com.

Macromolecule Content 

  • Total Structure Weight: 47.57 kDa 
  • Atom Count: 3,707 
  • Modeled Residue Count: 435 
  • Deposited Residue Count: 443 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D12 Fab heavy chain227Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
D12 Fab light chain216Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.220 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.962α = 90
b = 68.085β = 90
c = 102.993γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary