6VL9 | pdb_00006vl9

Anti-PEG antibody 6-3 Fab fragment in complex with PEG

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-01-23 Released: 2020-09-09 
  • Deposition Author(s): Nicely, N.I., Huckaby, J.T., Lai, S.K., Jacobs, T.M.
  • Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Science Foundation (NSF, United States), David and Lucile Packard Foundation, National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 
    0.250 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers

Huckaby, J.T., Jacobs, T.M., Li, Z., Perna, R.J., Wang, A., Nicely, N.I., Lai, S.K.

(2020) Commun Chem 3: 124


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-3 Fab heavy chainA [auth H],
C [auth A]		228Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
6-3 Fab light chainB [auth L],
D [auth B]		219Mus musculusMutation(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
9FO (Subject of Investigation/LOI)
Query on 9FO
Download Ideal Coordinates CCD File 
E [auth H]3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57-nonadecaoxanonapentacontane-1,59-diol
C40 H82 O21
ZHMUMDLGQBRJIW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free:  0.250 (Depositor) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.711α = 90
b = 169.788β = 90
c = 69.394γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesF32DE026683
National Science Foundation (NSF, United States)United StatesDMR-1810168
National Science Foundation (NSF, United States)United StatesDGE-1650116
David and Lucile Packard FoundationUnited States2013-39274
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL141934

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary