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- PDB-31np: Crystal structure of the complex of galectin-8N-2,6-anhydro-3-deo... -

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Basic information

Entry
Database: PDB / ID: 31np
TitleCrystal structure of the complex of galectin-8N-2,6-anhydro-3-deoxy-3-S-(beta-D-galactopyranosyl)-3-thio-D-glycero-L-altro-heptonamide
ComponentsGalectin-8
KeywordsSUGAR BINDING PROTEIN / galectin-8N
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / : / membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / 1-thio-beta-D-galactopyranose / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTsagkarakou, A.S. / Kantsadi, A.L. / Leonidas, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2026
Title: Structural and Biophysical Characterization of C-Glycosylic 1,2-Thiodisaccharides Reveals Determinants of Selective Binding to Galectin-7 and Galectin-8N.
Authors: Tsagkarakou, A.S. / Kantsadi, A.L. / Theodoridou, V.I. / Veliotis, N. / Lazar, L. / Jozsef, J. / Juhasz, L. / Kontopidis, G. / Leffler, H. / Nilsson, U.J. / Somsak, L. / Leonidas, D.D.
History
DepositionJun 15, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4425
Polymers35,8541
Non-polymers5884
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-1 kcal/mol
Surface area7910 Å2
Unit cell
Length a, b, c (Å)61.482, 40.201, 69.761
Angle α, β, γ (deg.)90.000, 115.076, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 35854.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00214
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-YIO / 1-thio-beta-D-galactopyranose / (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL / 1-thio-beta-D-galactose / 1-thio-D-galactose / 1-thio-galactose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Galp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-A1KB4 / (2~{R},3~{S},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxane-2-carboxamide


Mass: 207.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein at 10 mg/mL in PBS (pH 7.4) was mixed 1:1 with reservoir solution containing 0.1 M Tris/NaOAc (pH 5.6) 20% (v/v) 2-propanol and 20% PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2022
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.78→62 Å / Num. obs: 14804 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 32.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.5
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 832 / CC1/2: 0.797 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→27.84 Å / SU ML: 0.1896 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 686 4.64 %
Rwork0.1847 14114 -
obs0.1863 14800 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.92 Å2
Refinement stepCycle: LAST / Resolution: 1.78→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 37 80 1300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541260
X-RAY DIFFRACTIONf_angle_d0.81911706
X-RAY DIFFRACTIONf_chiral_restr0.0657191
X-RAY DIFFRACTIONf_plane_restr0.0083218
X-RAY DIFFRACTIONf_dihedral_angle_d14.6462477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.920.28381350.22672798X-RAY DIFFRACTION98.56
1.92-2.110.2381360.18592785X-RAY DIFFRACTION98.35
2.11-2.420.21471430.17612823X-RAY DIFFRACTION99.66
2.42-3.040.26461310.20692812X-RAY DIFFRACTION98.36
3.04-27.840.20161410.17532896X-RAY DIFFRACTION98.99
Refinement TLS params.Method: refined / Origin x: 19.368071663094 Å / Origin y: 5.110254410653 Å / Origin z: 10.888141752524 Å
111213212223313233
T0.23055378290876 Å2-0.014233993249739 Å20.00079252955672288 Å2-0.21448444064849 Å20.019985473169252 Å2--0.23603992978448 Å2
L2.8899580727096 °2-0.23684134873564 °2-0.3934647969057 °2-2.1664984506707 °20.15735746765962 °2--2.5416335456 °2
S0.046742242115466 Å °-0.13042276654261 Å °-0.17644519243469 Å °-0.024542296359533 Å °-0.024586509483181 Å °-0.018193874942487 Å °-0.01063681011347 Å °-0.094744496677524 Å °-0.0005478717129818 Å °
Refinement TLS groupSelection details: all

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