8IU1 | pdb_00008iu1

Crystal structure of mouse Galectin-3 in complex with small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb8IU1/pdb

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

Deposited: 2023-03-23 Released: 2024-03-27
Deposition Author(s): Jinal, S., Amit, K., Ghosh, K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.215 (Depositor), 0.214 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Discovery and Exploration of Monosaccharide Linked Dimers to Target Fibrosis

Swidorski, J.J., Beno, B.B., Liu, C., Yoon, D., Ghosh, K., Sale, H., Shah, D., Acharya, K., Yanchunas, J., Ellsworth, B., Cheng, D., Regueiro-Ren, A.

To be published.

Macromolecule Content

Total Structure Weight: 17.06 kDa
Atom Count: 1,240
Modeled Residue Count: 138
Deposited Residue Count: 146
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-3	A	146	Homo sapiens	Mutation(s): 0 Gene Names: Lgals3
UniProt
Find proteins for P16110 (Mus musculus) Explore P16110 Go to UniProtKB: P16110
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16110
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QB2 (Subject of Investigation/LOI) Query on QB2 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-[(2R,3R,4S,5R,6R)-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-yl]oxyethanoic acid C₂₂ H₁₈ Cl₂ F₃ N₃ O₆ S RROCGPVSGSQEET-WIXLDOGYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.215 (Depositor), 0.214 (DCC)
R-Value Work: 0.173 (Depositor), 0.174 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.67	α = 90
b = 110.67	β = 90
c = 110.67	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release

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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.