6VL8 | pdb_00006vl8

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

PDB DOI: https://doi.org/10.2210/pdb6VL8/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.240 (Depositor), 0.227 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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

Macromolecule Content

Total Structure Weight: 197.84 kDa
Atom Count: 13,788
Modeled Residue Count: 1,710
Deposited Residue Count: 1,788
Unique protein chains: 2

Macromolecules

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| 3D Structure

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

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| 3D Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEU (Subject of Investigation/LOI) Query on PEU Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain J [auth C] MOL2 format, chain L [auth E] MOL2 format, chain J [auth C] mmCIF format, chain L [auth E] mmCIF format, chain J [auth C]	J [auth C], L [auth E]	2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL C₅₅ H₁₁₂ O₂₈ ISGUIIHZEJGUGQ-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth E] Interactions & Density Focus chain J [auth C] Focus chain L [auth E]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth H] SDF format, chain K [auth D] SDF format, chain I [auth A] MOL2 format, chain M [auth H] MOL2 format, chain K [auth D] MOL2 format, chain I [auth A] mmCIF format, chain M [auth H] mmCIF format, chain K [auth D] mmCIF format, chain I [auth A]	I [auth A], K [auth D], M [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth D] Focus chain M [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth D] Focus chain M [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.240 (Depositor), 0.227 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.108	α = 90
b = 87.791	β = 113.655
c = 116.074	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

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 (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