6FK2 | pdb_00006fk2

Galectin-3 carbohydrate recognition domain in complex with lactitol

PDB DOI: https://doi.org/10.2210/pdb6FK2/pdb

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

Deposited: 2018-01-23 Released: 2019-02-06
Deposition Author(s): Doran, S.M.C., Faba Rodriguez, R., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.01 Å
R-Value Free:
0.141 (Depositor), 0.142 (DCC)
R-Value Work:
0.134 (Depositor), 0.135 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FK2

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

Literature

Ligand specificity at the D-site of human Galectin-3 Carbohydrate Recognition Domain

Doran, S.M.C., Faba Rodriguez, R., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 16.05 kDa
Atom Count: 1,343
Modeled Residue Count: 138
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-sorbitol	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G26039ES GlyCosmos: G26039ES GlyGen: G26039ES

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.01 Å
R-Value Free: 0.141 (Depositor), 0.142 (DCC)
R-Value Work: 0.134 (Depositor), 0.135 (DCC)
R-Value Observed: 0.134 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.295	α = 90
b = 57.631	β = 90
c = 62.604	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Faba Rodriguez, R.

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary

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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.