5IUQ | pdb_00005iuq

Galectin-3c in complex with Bisamido-thiogalactoside derivative 4

PDB DOI: https://doi.org/10.2210/pdb5IUQ/pdb

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

Deposited: 2016-03-18 Released: 2017-03-29
Deposition Author(s): Noresson, A.-L., Aurelius, O., Oberg, C.T., Engstrom, O., Sundin, A.P., Hakansson, M., Logan, D.T., Leffler, H., Nilsson, U.J.
Funding Organization(s): Swedish Research Council, Olle Engkvist Byggmastare foundation, Royal Physiographic Society, European Community's Seventh Framework Program (FP7-2007-2013)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free:
0.172 (Depositor), 0.183 (DCC)
R-Value Work:
0.153 (Depositor), 0.165 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Controlling protein:ligand complex conformation through tuning of arginine-arene interactions: Synthetic and structural studies with 3-benzamido-2-sulfo-galactosides as galectin-3 ligands

Noresson, A.-L., Aurelius, O., Oberg, C.T., Engstrom, O., Sundin, A.P., Hakansson, M., Logan, D., Leffler, H., Nilsson, U.J.

To be published.

Macromolecule Content

Total Structure Weight: 16.47 kDa
Atom Count: 1,492
Modeled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 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 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6E1 Query on 6E1 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]	3-deoxy-3-[(2,3,5,6-tetrafluoro-4-methoxybenzene-1-carbonyl)amino]-beta-D-galactopyranosyl 3-deoxy-3-[(2,3,5,6-tetrafluoro-4-methoxybenzene-1-carbonyl)amino]-1-thio-beta-D-galactopyranoside C₂₈ H₂₈ F₈ N₂ O₁₂ S ZLQVWZMNOBVEMR-RIEDQWIWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 Å
R-Value Free: 0.172 (Depositor), 0.183 (DCC)
R-Value Work: 0.153 (Depositor), 0.165 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.064	α = 90
b = 57.553	β = 90
c = 62.202	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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: 2017-03-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	621-2009-5326
Swedish Research Council	Sweden	621-2012-2978
Olle Engkvist Byggmastare foundation	Sweden	--
Royal Physiographic Society	Sweden	--
European Community's Seventh Framework Program (FP7-2007-2013)		HEALTH F2-2011-256986 project acronym PANACREAS

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2018-01-17
Changes: Data collection
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description