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- PDB-31nv: Crystal structure of the complex of galectin-8N-TDG -

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Basic information

Entry
Database: PDB / ID: 31nv
TitleCrystal structure of the complex of galectin-8N-TDG
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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)36,2122
Polymers35,8541
Non-polymers3581
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint2 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.030, 39.194, 55.734
Angle α, β, γ (deg.)90.000, 107.483, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-560-

HOH

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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: Polysaccharide 1-thio-beta-D-galactopyranose-(1-1)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 358.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/1,2,1/[a2112h-1b_1-5]/1-1/a1-b1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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, sitting drop / pH: 5.6
Details: Galecin-8N 10 mg/mL in PBS (pH 7.4) was mixed 1:1 with reservoir solution containing 0.1 M Tris/sodium citrate (pH 5.6), 20% (v/v) 2- propanol, 20 % (w/v) PEG4000 and 1 mM TDG.

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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: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.71→60 Å / Num. obs: 12509 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 25.48 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.214 / Net I/σ(I): 6
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.306 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 573 / CC1/2: 0.503 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→29.89 Å / SU ML: 0.2282 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9124
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2926 615 4.93 %
Rwork0.2407 11868 -
obs0.2432 12483 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.2 Å2
Refinement stepCycle: LAST / Resolution: 1.71→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 23 66 1264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00391250
X-RAY DIFFRACTIONf_angle_d0.71381697
X-RAY DIFFRACTIONf_chiral_restr0.0561191
X-RAY DIFFRACTIONf_plane_restr0.0061218
X-RAY DIFFRACTIONf_dihedral_angle_d16.2832509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.880.32071520.30022916X-RAY DIFFRACTION93
1.88-2.150.28871310.27492919X-RAY DIFFRACTION92.45
2.15-2.710.33431660.27793006X-RAY DIFFRACTION94.71
2.71-29.890.2721660.21253027X-RAY DIFFRACTION93.99
Refinement TLS params.Method: refined / Origin x: 14.680751654006 Å / Origin y: 5.583287154438 Å / Origin z: 11.982811510896 Å
111213212223313233
T0.43500771855236 Å20.047642404028681 Å2-0.089326166766349 Å2-0.31405461321023 Å20.01221296520077 Å2---0.034970770721143 Å2
L2.7121522042509 °2-0.18894067981696 °20.84741189804595 °2-4.1445911813697 °2-1.4335857865633 °2--4.9888266151269 °2
S-0.08606345081977 Å °0.19701519260273 Å °0.082369610133839 Å °-0.55813467775625 Å °-0.043777173538367 Å °0.068661009465295 Å °0.28713633988474 Å °-0.082611415756249 Å °0.086829458697591 Å °
Refinement TLS groupSelection details: (chain A and resseq 8:154)

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