4LBL

Crystal structure of Human galectin-3 CRD K176L mutant in complex with a-GM3

PDB DOI: https://doi.org/10.2210/pdb4LBL/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-06-20 Released: 2014-01-22
Deposition Author(s): Bum-Erdene, K., Blanchard, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.190
R-Value Work: 0.153
R-Value Observed: 0.155

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 16.42 kDa
Atom Count: 1,405
Modelled Residue Count: 138
Deposited Residue Count: 138
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-3	A	138	Homo sapiens	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17931
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G91237TK GlyCosmos: G91237TK GlyGen: G91237TK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.190
R-Value Work: 0.153
R-Value Observed: 0.155
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.86	α = 90
b = 57.61	β = 90
c = 62.59	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Bum-Erdene, K.

Blanchard, H.

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2014-03-26
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

4LBL

Crystal structure of Human galectin-3 CRD K176L mutant in complex with a-GM3

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)