6F83

Crystal Structure of Human Galectin-1 in Complex With Thienyl-1,2, 3-triazolyl Thiodigalactoside Inhibitor

PDB DOI: https://doi.org/10.2210/pdb6F83/pdb

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

Deposited: 2017-12-12 Released: 2019-01-30
Deposition Author(s): Collins, P.M., Blanchard, H.
Funding Organization(s): Cancer Council Queensland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.224
R-Value Work: 0.171
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Aromatic heterocycle galectin-1 interactions for selective single-digit nM affinity ligands

Peterson, A., Collins, P.M., Kahl-Knutsson, B., Zetterberg, F.R., Blanchard, H., Leffler, H., Nilsson, U.J.

To be published.

Macromolecule Content

Total Structure Weight: 31.21 kDa
Atom Count: 2,315
Modelled Residue Count: 268
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-1	A, B	134	Homo sapiens	Mutation(s): 0 Gene Names: LGALS1
UniProt & NIH Common Fund Data Resources
Find proteins for P09382 (Homo sapiens) Explore P09382 Go to UniProtKB: P09382
PHAROS: P09382 GTEx: ENSG00000100097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09382
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5KT (Subject of Investigation/LOI) Query on 5KT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	3-deoxy-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-1-thio-3-[4-(thiophen-3-yl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranoside C₂₄ H₂₈ N₆ O₈ S₃ OYKAQKLJBYMZSV-VLLPDFJVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.224
R-Value Work: 0.171
R-Value Observed: 0.173
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.447	α = 90
b = 58.689	β = 90
c = 112.353	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Council Queensland	Australia	ID1080845

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.