Macromolecule Content

Total Structure Weight: 16.29 kDa
Atom Count: 1,369
Modelled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

7BE3

Human Galectin-3 in complex with LacdiNAc

PDB DOI: https://doi.org/10.2210/pdb7BE3/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-12-22 Released: 2021-04-21
Deposition Author(s): Trovao, F., Carvalho, A.L.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.170
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

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

Literature

Structural Insights into the Molecular Recognition Mechanism of the Cancer and Pathogenic Epitope, LacdiNAc by Immune-Related Lectins.

Lima, C.D.L., Coelho, H., Gimeno, A., Trovao, F., Diniz, A., Dias, J.S., Jimenez-Barbero, J., Corzana, F., Carvalho, A.L., Cabrita, E.J., Marcelo, F.

(2021) Chemistry 27: 7951-7958

PubMed: 33826192 Search on PubMed
DOI: https://doi.org/10.1002/chem.202100800
Primary Citation of Related Structures:
7BE3

PubMed Abstract:

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	138	Homo sapiens	Mutation(s): 0 Gene Names: LGALS3, MAC2
UniProt & NIH Common Fund Data Resources
Find proteins for P17931 (Homo sapiens) Explore P17931 Go to UniProtKB: P17931
PHAROS: P17931
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17931
Protein Feature View Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	B [auth C]	2	N/A	N/A	Oligosaccharides Interaction

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.195
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.039	α = 90
b = 58.048	β = 90
c = 62.286	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-04-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Foundation for Science and Technology (FCT)	Portugal	--

Revision History (Full details and data files)

Version 1.0: 2021-04-21
Type: Initial release
Version 1.1: 2021-06-02
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.