6H3H

Fab fragment of antibody against fullerene C60


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the Anti-C60 Fullerene Antibody Fab Fragment: Structural Determinants of Fullerene Binding.

Osipov, E.M.Hendrickson, O.D.Tikhonova, T.V.Zherdev, A.V.Solopova, O.N.Sveshnikov, P.G.Dzantiev, B.B.Popov, V.O.

(2019) Acta Naturae 11: 58-65


  • PubMed Abstract: 
  • The structure of the anti-C <sub>60 </sub> fullerene antibody Fab fragment (FabC <sub>60 </sub>) was solved by X-ray crystallography. The computer-aided docking of C <sub>60 </sub> into the antigen-binding pocket of FabC <sub>60 </sub> showed that bi ...

    The structure of the anti-C 60 fullerene antibody Fab fragment (FabC 60 ) was solved by X-ray crystallography. The computer-aided docking of C 60 into the antigen-binding pocket of FabC 60 showed that binding of C 60 to FabC 60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding site and reduction of the solvent-accessible area of the hydrophobic surface of C 60 . A fragment of the mobile CDR H3 loop located on the surface of FabC 60 interferes with C 60 binding in the antigen-binding site, thereby resulting in low antibody affinity for C 60 . The structure of apo-FabC 60 has been deposited with pdbid 6H3H.


    Organizational Affiliation

    Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia.,Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-fullerene antibody Fab fragment Heavy chain
A, C
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-fullerene antibody Fab fragment Light chain
B, D
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.330α = 90.00
b = 138.180β = 91.85
c = 83.530γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
BALBESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation14-24-00172

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release