7V64 | pdb_00007v64

Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)

PDB DOI: https://doi.org/10.2210/pdb7V64/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Trichopalpus nigribasis
Mutation(s): No

Deposited: 2021-08-19 Released: 2022-08-24
Deposition Author(s): Niu, J., Xu, L., Meng, B., Han, Y.B., Yang, B.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.203 (Depositor), 0.206 (DCC)
R-Value Work:
0.179 (Depositor), 0.184 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Site-specific GalNAc modification on a MUC1 neoantigen epitope forms a basis for high-affinity antibody binding

Han, Y.B., Xu, L.

To be published.

Macromolecule Content

Total Structure Weight: 49.73 kDa
Atom Count: 3,835
Modeled Residue Count: 434
Deposited Residue Count: 459
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
16A fab Light chain	A	217	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
16A fab Heavy chain	B	229	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1 subunit alpha	C	13	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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NGA (Subject of Investigation/LOI) Query on NGA 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-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.203 (Depositor), 0.206 (DCC)
R-Value Work: 0.179 (Depositor), 0.184 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.534	α = 90
b = 81.225	β = 90
c = 137.331	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.