8JAE | pdb_00008jae

Crystal structure of E33A mutant human galectin-10 produced by cell-free protein synthesis in complex with melezitose

PDB DOI: https://doi.org/10.2210/pdb8JAE/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Triticum aestivum
Mutation(s): Yes

Deposited: 2023-05-05 Released: 2024-05-08
Deposition Author(s): Kojima, M., Ueno, T., Abe, S., Hirata, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.222 (Depositor), 0.220 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Cell-Free Protein Crystallization Enables Rapid Structure Determination of Disaccharides and Trisaccharides Using Galectin-10 Crystals.

Kojima, M., Yao, X., Abe, S., Furuta, T., Hirata, K., Kobayashi, R., Suzuki, T., Ueno, T.

(2025) Small Struct

DOI: https://doi.org/10.1002/sstr.202500501

Macromolecule Content

Total Structure Weight: 16.92 kDa
Atom Count: 1,365
Modeled Residue Count: 140
Deposited Residue Count: 142
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-10	A	142	Homo sapiens	Mutation(s): 1 Gene Names: CLC, LGALS10, LGALS10A
UniProt & NIH Common Fund Data Resources
Find proteins for Q05315 (Homo sapiens) Explore Q05315 Go to UniProtKB: Q05315
PHAROS: Q05315 GTEx: ENSG00000105205
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05315
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-2)-[alpha-D-glucopyranose-(1-3)]beta-D-fructofuranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G80689JY GlyCosmos: G80689JY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.222 (Depositor), 0.220 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.16	α = 90
b = 49.16	β = 90
c = 262.56	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-05-08
Type: Initial release
Version 1.1: 2024-07-17
Changes: Source and taxonomy
Version 1.2: 2026-02-18
Changes: Database references, Structure summary

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.