6RZK | pdb_00006rzk

Galectin-3C in complex with trifluoroaryltriazole monothiogalactoside derivative:3(Chlorine)

PDB DOI: https://doi.org/10.2210/pdb6RZK/pdb

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

Deposited: 2019-06-13 Released: 2020-07-08
Deposition Author(s): Kumar, R., Verteramo, M.L., Nilsson, U.J., Logan, D.T.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free:
0.150 (Depositor), 0.154 (DCC)
R-Value Work:
0.124 (Depositor), 0.128 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Thermodynamic studies of halogen-bond interactions in galectin-3

Verteramo, M.L., Zetterberg, F., Kumar, R., Wallerstein, J., Ignjatovic, M.M., Leffler, H., Ryde, U., Logan, D.T., Akke, M., Nilsson, U.J.

To be published.

Macromolecule Content

Total Structure Weight: 16.22 kDa
Atom Count: 1,538
Modeled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

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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
KOZ (Subject of Investigation/LOI) Query on KOZ 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})-2-(3-chlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol C₂₀ H₁₇ Cl F₃ N₃ O₄ S MJHCQQXAUYYTBY-DABHTEOTSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-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: 1.05 Å
R-Value Free: 0.150 (Depositor), 0.154 (DCC)
R-Value Work: 0.124 (Depositor), 0.128 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.91	α = 90
b = 57.751	β = 90
c = 63.025	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Verteramo, M.L.

Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	KAW 2013.0022

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.