8RRC | pdb_00008rrc

Galectin-3 with a small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb8RRC/pdb

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

Deposited: 2024-01-22 Released: 2025-01-29
Deposition Author(s): Mac Sweeney, A., Sager, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8RRC

Ligand Structure Quality Assessment

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

Literature

Galectin-3 with a small molecule inhibitor

Remen, L., Zumbrunn, C., Sager, C.P., Grisostomi, C., Mac Sweeney, A., Gatfield, J., Huehn, E., Vercauteren, E., Fournier, E., Schmidt, G., Davenport, R., Iglarz, M., Nayler, O., Bolli, M.H.

To be published.

Macromolecule Content

Total Structure Weight: 16.29 kDa
Atom Count: 1,250
Modeled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 GTEx: ENSG00000131981
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H2O (Subject of Investigation/LOI) Query on A1H2O 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~{R},3~{R},4~{S},5~{R},6~{R})-4-[4-[4-chloranyl-2,3-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-5-methoxy-6-[[3-(3-methyloxetan-3-yl)-1,2-oxazol-5-yl]methyl]oxan-3-ol C₂₃ H₂₅ Cl F₂ N₄ O₆ WTCIDOBGJUDIAX-IVZPRWNWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SCN Query on SCN 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]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.804	α = 90
b = 57.28	β = 90
c = 61.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-29

Deposition Author(s):

Mac Sweeney, A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-29
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.