6KX0 | pdb_00006kx0

Crystal structure of SN-101 mAb non-liganded form

PDB DOI: https://doi.org/10.2210/pdb6KX0/pdb

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

Deposited: 2019-09-09 Released: 2020-07-29
Deposition Author(s): Wakui, H., Tanaka, Y., Kato, K., Ose, T., Matsumoto, I., Min, Y., Tachibana, T., Nishimura, S.-I.
Funding Organization(s): Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.225 (Depositor), 0.226 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes

Wakui, H., Tanaka, Y., Ose, T., Matsumoto, I., Kato, K., Min, Y., Tachibana, T., Sato, M., Naruchi, K., Martin, F.G., Hinou, H., Nishimura, S.-I.

(2020) Chem Sci 11: 4999-5006

DOI: https://doi.org/10.1039/D0SC00317D

Macromolecule Content

Total Structure Weight: 52.22 kDa
Atom Count: 3,348
Modeled Residue Count: 429
Deposited Residue Count: 475
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Fragment-SN-101-Heavy chain	A	236	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Fragment-SN-101-Light chain	B	239	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.278 (Depositor), 0.278 (DCC)
R-Value Work: 0.225 (Depositor), 0.226 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.86	α = 90
b = 40.1	β = 99.83
c = 67.78	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	25220206
Japan Society for the Promotion of Science	Japan	19H00918

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary