6VL9

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

• PDB DOI: https://doi.org/10.2210/pdb6VL9/pdb

• 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)

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Experimental Data Snapshot

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

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

• DOI: https://doi.org/10.1038/s42004-020-00369-y

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.51 kDa 
• Atom Count: 6,833 
• Modelled Residue Count: 854 
• Deposited Residue Count: 894 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-3 Fab heavy chain	A [auth H], C [auth A]	228	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
6-3 Fab light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9FO (Subject of Investigation/LOI)	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 
• R-Value Work: 0.178 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.711	α = 90
b = 169.788	β = 90
c = 69.394	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Currently 6VL9 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-09 
Deposition Author(s): Nicely, N.I., Huckaby, J.T., Lai, S.K., Jacobs, T.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	F32DE026683
National Science Foundation (NSF, United States)	United States	DMR-1810168
National Science Foundation (NSF, United States)	United States	DGE-1650116
David and Lucile Packard Foundation	United States	2013-39274
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL141934

Revision History  

• 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