6JU0

Mouse antibody 3.3 Fab in complex with PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of polyethylene glycol recognition by antibody.

Lee, C.C.Su, Y.C.Ko, T.P.Lin, L.L.Yang, C.Y.Chang, S.S.Roffler, S.R.Wang, A.H.

(2020) J.Biomed.Sci. 27: 12-12

  • DOI: 10.1186/s12929-019-0589-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyethylene glycol (PEG) is widely used in industry and medicine. Anti-PEG antibodies have been developed for characterizing PEGylated drugs and other applications. However, the underlying mechanism for specific PEG binding has not been elucidated.

    Polyethylene glycol (PEG) is widely used in industry and medicine. Anti-PEG antibodies have been developed for characterizing PEGylated drugs and other applications. However, the underlying mechanism for specific PEG binding has not been elucidated.


    Organizational Affiliation

    Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. ahjwang@gate.sinica.edu.tw.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan. chengung@gate.sinica.edu.tw.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. sroff@ibms.sinica.edu.tw.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Medigen Biotechnology Corporation, Taipei, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
H, I, J, K
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
L, M, N, O
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
K
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
TOE
Query on TOE

Download SDF File 
Download CCD File 
H, I, J, K
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
H
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PE3
Query on PE3

Download SDF File 
Download CCD File 
I, K
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
POLYETHYLENE GLYCOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
L, M, N, O
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.299α = 90.00
b = 177.347β = 91.99
c = 89.019γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release