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- PDB-8r74: Galectin-1 in complex with thiogalactoside derivative -

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Basic information

Entry
Database: PDB / ID: 8r74
TitleGalectin-1 in complex with thiogalactoside derivative
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / galectin / ligand / thiogalactoside derivative
Function / homology
Function and homology information


galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol
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: 1.54 Å
AuthorsHakansson, M. / Diehl, C. / Peterson, K. / Zetterberg, F. / Nilsson, U.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of the Selective and Orally Available Galectin-1 Inhibitor GB1908 as a Potential Treatment for Lung Cancer.
Authors: Zetterberg, F.R. / Peterson, K. / Nilsson, U.J. / Andreasson Dahlgren, K. / Diehl, C. / Holyer, I. / Hakansson, M. / Khabut, A. / Kahl-Knutson, B. / Leffler, H. / MacKinnon, A.C. / Roper, J. ...Authors: Zetterberg, F.R. / Peterson, K. / Nilsson, U.J. / Andreasson Dahlgren, K. / Diehl, C. / Holyer, I. / Hakansson, M. / Khabut, A. / Kahl-Knutson, B. / Leffler, H. / MacKinnon, A.C. / Roper, J.A. / Slack, R.J. / Zarrizi, R. / Pedersen, A.
History
DepositionNov 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4444
Polymers29,4612
Non-polymers9832
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-3 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.139, 62.352, 98.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 134 / Label seq-ID: 3 - 135

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 14730.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Chemical ChemComp-YBC / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-4-[4-(2-oxidanyl-1,3-thiazol-4-yl)-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 491.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C17H16Cl2N4O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate pH 6.2, 29 % PEG 4000, 0.2 M ammonium sulphate, seeded

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→46.72 Å / Num. obs: 48869 / % possible obs: 99.9 % / Redundancy: 4.24 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10
Reflection shellResolution: 1.54→1.57 Å / Rmerge(I) obs: 0.76 / Num. unique obs: 15024 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→46.715 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.585 / SU ML: 0.092 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2189 2453 5.02 %
Rwork0.1752 46416 -
all0.177 --
obs-48869 99.814 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.666 Å2
Baniso -1Baniso -2Baniso -3
1-2.112 Å2-0 Å20 Å2
2--0.725 Å2-0 Å2
3----2.836 Å2
Refinement stepCycle: LAST / Resolution: 1.54→46.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 60 221 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162124
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.853163
X-RAY DIFFRACTIONr_angle_other_deg0.6551.7694908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5545301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.932511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1910362
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.63810110
X-RAY DIFFRACTIONr_chiral_restr0.0870.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022834
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02550
X-RAY DIFFRACTIONr_nbd_refined0.2160.2330
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.21760
X-RAY DIFFRACTIONr_nbtor_refined0.180.21040
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.21187
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2960.27
X-RAY DIFFRACTIONr_nbd_other0.2480.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.221
X-RAY DIFFRACTIONr_mcbond_it3.9931.6531143
X-RAY DIFFRACTIONr_mcbond_other3.9911.6531143
X-RAY DIFFRACTIONr_mcangle_it5.6872.9691448
X-RAY DIFFRACTIONr_mcangle_other5.6862.9681449
X-RAY DIFFRACTIONr_scbond_it5.1751.8451163
X-RAY DIFFRACTIONr_scbond_other5.1021.8421160
X-RAY DIFFRACTIONr_scangle_it7.1123.3161710
X-RAY DIFFRACTIONr_scangle_other7.0963.3131708
X-RAY DIFFRACTIONr_lrange_it11.43822.0869459
X-RAY DIFFRACTIONr_lrange_other10.88720.99282
X-RAY DIFFRACTIONr_rigid_bond_restr6.18934430
X-RAY DIFFRACTIONr_ncsr_local_group_10.1170.054142
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.11660.05008
12AX-RAY DIFFRACTIONLocal ncs0.11660.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.54-1.580.4051670.41433530.41435520.7980.81199.09910.398
1.58-1.6230.3911790.37632890.37734710.8720.86699.91360.354
1.623-1.670.3871720.34232180.34433920.9280.95699.9410.311
1.67-1.7210.3611800.30131150.30432970.9310.96699.93930.266
1.721-1.7780.2981390.26930630.27132040.9740.97599.93760.226
1.778-1.840.3051450.2329370.23330830.9720.98199.96760.19
1.84-1.9090.2381580.19828310.229920.9690.98699.89970.159
1.909-1.9870.2161470.1627230.16328720.9820.99199.93040.128
1.987-2.0750.1861370.15226240.15327620.9850.99199.96380.125
2.075-2.1760.2181240.15725110.15926390.9720.98999.84840.136
2.176-2.2940.191360.14624070.14825440.9810.9999.96070.127
2.294-2.4330.2351230.15522630.15923900.9720.98899.83260.14
2.433-2.60.2081100.15921440.16222620.980.98799.64630.147
2.6-2.8080.2081170.14719880.1521060.9770.98899.95250.139
2.808-3.0750.201990.15718510.15919520.9740.98699.89750.155
3.075-3.4360.189780.15716990.15817780.980.98799.94380.159
3.436-3.9640.184860.15214890.15415790.9790.98899.74670.161
3.964-4.8460.177760.12812870.13113640.9840.99199.92670.142
4.846-6.8160.212440.18210210.18410730.9810.98699.25440.2
6.816-46.7150.239360.1896030.1916460.9720.97798.91640.213
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.60540.3909-0.42421.7411-0.17621.4868-0.12630.02990.0259-0.13150.00350.0511-0.0152-0.0890.12280.01370.0006-0.00550.04020.01560.178129.7824-14.7189-6.8726
21.8404-0.73950.66622.525-1.66333.6742-0.0628-0.2556-0.03180.13970.2933-0.06630.0012-0.5629-0.23050.0275-0.0041-0.03560.22450.03830.23168.8549-1.5656-21.2577
Refinement TLS groupSelection: ALL

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