6KX1 | pdb_00006kx1

Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide

PDB DOI: https://doi.org/10.2210/pdb6KX1/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
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: 1.77 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 53.66 kDa
Atom Count: 3,619
Modeled Residue Count: 440
Deposited Residue Count: 491
Unique protein chains: 3

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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic MUC1 glycopepide	C	16	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941
PHAROS: P15941 GTEx: ENSG00000185499
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15941
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C	Go to GlyGen: P15941-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G (Subject of Investigation/LOI) Query on A2G Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.92	α = 90
b = 39.98	β = 100.56
c = 63.87	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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: 2020-07-29

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, Structure summary
Version 1.2: 2024-11-20
Changes: Structure summary