8IQP

Crystal structure of Anti-PEG antibody M9 Fv-clasp fragment with PEG (co-crystallization with PEG3350)

PDB DOI: https://doi.org/10.2210/pdb8IQP/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-03-17 Released: 2024-03-20
Deposition Author(s): Mori, T., Teramoto, T., Liu, Y., Mori, T., Kakuta, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.246
R-Value Work: 0.205
R-Value Observed: 0.206

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Comparation of structures and binding properties between two anti-polyethylene glycol antibodies induced via T cell-independent and T cell-dependent pathway

Liu, Y., Mori, T., Teramoto, T., Kakuta, Y., Mori, T.

To be published.

Macromolecule Content

Total Structure Weight: 83.49 kDa
Atom Count: 5,846
Modelled Residue Count: 670
Deposited Residue Count: 728
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
M9 VL-SARAH	A [auth L], C [auth l]	179	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M9 VH-SARAH	B [auth H], D [auth h]	185	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P (Subject of Investigation/LOI) Query on 12P Download Ideal Coordinates CCD File SDF format, chain E [auth H] SDF format, chain F [auth h] MOL2 format, chain E [auth H] MOL2 format, chain F [auth h] mmCIF format, chain E [auth H] mmCIF format, chain F [auth h]	E [auth H], F [auth h]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth h] Interactions & Density Focus chain E [auth H] Focus chain F [auth h]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.246
R-Value Work: 0.205
R-Value Observed: 0.206
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.23	α = 90
b = 68.34	β = 104.2
c = 94.79	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-03-20
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.