5YD3

Crystal structure of the scFv antibody 4B08 with epitope peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody

Miyanabe, K.Akiba, H.Kuroda, D.Nakakido, M.Kusano-Arai, O.Iwanari, H.Hamakubo, T.Caaveiro, J.M.M.Tsumoto, K.

(2018) J. Biochem. 164: 65-76

  • DOI: 10.1093/jb/mvy032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity ...

    Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.


    Organizational Affiliation

    Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
scFv 4B08
A, C, E, G
251Mus musculusMutation(s): 0 
Find proteins for P01630 (Mus musculus)
Go to UniProtKB:  P01630
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Epitope peptide
B, D, F, H
9Homo sapiensMutation(s): 0 
Gene Names: CCR5 (CMKBR5)
Find proteins for P51681 (Homo sapiens)
Go to Gene View: CCR5
Go to UniProtKB:  P51681
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, G
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
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: 1.35 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.480α = 90.00
b = 72.970β = 114.30
c = 86.990γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan25249115
Japan Society for the Promotion of ScienceJapan15K06962

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references