9UDR | pdb_00009udr

Single-chain Fv antibody of B2 complex with NP-glycine

PDB DOI: https://doi.org/10.2210/pdb9UDR/pdb

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

Deposited: 2025-04-07 Released: 2025-11-05
Deposition Author(s): Yoshida, M., Hanazono, Y., Numoto, N., Ito, N., Oda, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free:
0.163 (Depositor), 0.163 (DCC)
R-Value Work:
0.151 (Depositor), 0.151 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during affinity maturation

Yoshida, M., Hanazono, Y., Numoto, N., Yabuno, S., Ito, N., Azuma, T., Oda, M.

To be published.

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 2,256
Modeled Residue Count: 230
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-chain Fv antibody of B2	A	245	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
A1LZO (Subject of Investigation/LOI) Query on A1LZO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-[2-(3-nitro-4-oxidanyl-phenyl)ethanoylamino]ethanoic acid C₁₀ H₁₀ N₂ O₆ GTYVYDYXIPPDBJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.34 Å
R-Value Free: 0.163 (Depositor), 0.163 (DCC)
R-Value Work: 0.151 (Depositor), 0.151 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.039	α = 90
b = 71.834	β = 90
c = 82.054	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-05
Type: Initial release

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.