3I8T | pdb_00003i8t

N-terminal CRD1 domain of mouse Galectin-4 in complex with lactose

PDB DOI: https://doi.org/10.2210/pdb3I8T/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-10 Released: 2011-02-23
Deposition Author(s): Brynda, J., Krejcirikova, V., Rezacova, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.224 (Depositor), 0.277 (DCC)
R-Value Work:
0.187 (Depositor), 0.235 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structure of the mouse galectin-4 N-terminal carbohydrate-recognition domain reveals the mechanism of oligosaccharide recognition

Krejcirikova, V., Pachl, P., Fabry, M., Maly, P., Rezacova, P., Brynda, J.

(2011) Acta Crystallogr D Biol Crystallogr 67: 204-211

PubMed: 21358051 Search on PubMed
DOI: https://doi.org/10.1107/S0907444911004082
Primary Citation Related Structures:
3I8T

PubMed Abstract:
Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 Å resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a K(d) value in the micromolar range (K(d1) = 600 ± 70 µM) and a low-affinity site with K(d2) = 28 ± 10 mM.

Organizational Affiliation

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, vvi, Prague, Czech Republic.

Macromolecule Content

Total Structure Weight: 19.44 kDa
Atom Count: 1,302
Modeled Residue Count: 140
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-4	A	164	Mus musculus	Mutation(s): 0 Gene Names: gal-4, Lgals4
UniProt
Find proteins for Q8K419 (Mus musculus) Explore Q8K419 Go to UniProtKB: Q8K419
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8K419
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G88362QR GlyCosmos: G88362QR GlyGen: G88362QR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008 Query on PRD_900008	B	alpha-lactose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.224 (Depositor), 0.277 (DCC)
R-Value Work: 0.187 (Depositor), 0.235 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.841	α = 90
b = 90.841	β = 90
c = 57.104	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Brynda, J.

Krejcirikova, V.

Rezacova, P.

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-11-30
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary