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- PDB-8ojp: Human galectin 1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 8ojp
TitleHuman galectin 1 in complex with inhibitor
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / galectin / ligand / complex / sugar binding
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / myoblast differentiation / plasma cell differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of inflammatory response / : / regulation of apoptotic process / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of apoptotic process / receptor ligand activity / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / plasma membrane / 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: 1.71 Å
AuthorsHakansson, M. / Diehl, C. / Nilsson, U.J. / Zetterberg, F.R. / Peterson, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of Selective and Orally Available Galectin-1 Inhibitors.
Authors: Zetterberg, F.R. / Diehl, C. / Hakansson, M. / Kahl-Knutson, B. / Leffler, H. / Nilsson, U.J. / Peterson, K. / Roper, J.A. / Slack, R.J.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,9975
Polymers29,9182
Non-polymers1,0793
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area11590 Å2
Unit cell
Length a, b, c (Å)53.350, 61.960, 100.730
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: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 3 - 133 / Label seq-ID: 4 - 134

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: 14959.027 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-VPZ / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-[3,5-bis(chloranyl)-4-fluoranyl-phenyl]sulfanyl-6-(hydroxymethyl)-4-[4-(1,3-thiazol-2-yl)-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 493.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15Cl2FN4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8, 28% PEG3350, 0.1 M Li2SO4, 1% beta-mercapthoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.71→52.78 Å / Num. obs: 36768 / % possible obs: 99.8 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Net I/σ(I): 20.3
Reflection shellResolution: 1.71→1.74 Å / Rmerge(I) obs: 0.672 / Num. unique obs: 2200 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→52.775 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.164 / SU B: 4.623 / SU ML: 0.071 / Average fsc free: 0.9639 / Average fsc work: 0.9728 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.094
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2063 1863 5.067 %
Rwork0.1675 34905 -
all0.169 --
obs-36768 99.799 %
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: 30.499 Å2
Baniso -1Baniso -2Baniso -3
1--1.615 Å20 Å20 Å2
2--2.583 Å2-0 Å2
3----0.968 Å2
Refinement stepCycle: LAST / Resolution: 1.71→52.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 66 222 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122233
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162057
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.6813036
X-RAY DIFFRACTIONr_angle_other_deg0.6371.5914747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4325279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.444511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62810341
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.72510106
X-RAY DIFFRACTIONr_chiral_restr0.3250.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_nbd_refined0.2030.2303
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21806
X-RAY DIFFRACTIONr_nbtor_refined0.180.21045
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.2175
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1970.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.24
X-RAY DIFFRACTIONr_nbd_other0.1660.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.215
X-RAY DIFFRACTIONr_mcbond_it2.2982.1411088
X-RAY DIFFRACTIONr_mcbond_other2.2982.1411088
X-RAY DIFFRACTIONr_mcangle_it3.3493.8171363
X-RAY DIFFRACTIONr_mcangle_other3.3483.8161364
X-RAY DIFFRACTIONr_scbond_it3.7572.5961145
X-RAY DIFFRACTIONr_scbond_other3.7572.5961145
X-RAY DIFFRACTIONr_scangle_it5.6414.5481669
X-RAY DIFFRACTIONr_scangle_other5.6394.5471670
X-RAY DIFFRACTIONr_lrange_it7.75824.3522351
X-RAY DIFFRACTIONr_lrange_other7.68522.6392296
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.054064
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098040.05009
12AX-RAY DIFFRACTIONLocal ncs0.098040.05009
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
1.71-1.7540.2981330.26825480.2726810.9260.9321000.25
1.754-1.8020.2361230.23324780.23326040.9450.95199.88480.202
1.802-1.8550.2591170.22524320.22625530.9290.95399.84330.192
1.855-1.9120.2561130.20223570.20424730.9550.96899.87870.164
1.912-1.9740.2041380.18622660.18724060.9710.97499.91690.146
1.974-2.0430.2161140.16822060.1723230.9720.97699.87090.133
2.043-2.120.1971180.17120970.17222180.9680.97799.86470.136
2.12-2.2070.21180.16120670.16321870.9740.98299.90850.13
2.207-2.3050.1851140.15319570.15520750.9680.98299.80720.125
2.305-2.4170.21010.16318950.16520020.9720.98299.70030.138
2.417-2.5480.203990.15918010.16119000.9720.9831000.137
2.548-2.7020.19940.15417130.15618100.9780.98499.83430.139
2.702-2.8880.236900.15115880.15516870.9680.98599.46650.141
2.888-3.1180.208910.16614940.16815910.9740.98399.62290.163
3.118-3.4150.211700.16913980.17114680.9750.9841000.173
3.415-3.8160.192680.16112720.16313440.9820.98699.70240.174
3.816-4.4020.139480.12811300.12911890.9890.9999.07490.147
4.402-5.3820.168530.1429690.14410260.9830.9999.61010.178
5.382-7.5720.291370.2147740.2188140.9660.97999.63150.243
7.572-52.7750.319240.2224630.2264910.9560.96699.18530.285
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)
12.55130.40670.19431.3943-0.10951.0959-0.06380.0498-0.0991-0.05120.0072-0.08530.03690.07950.05660.02660.00350.01320.00680.00250.0127-29.376514.3632-6.9488
21.3116-0.0955-0.45631.80030.32952.61070.0146-0.13210.05680.11770.14790.0403-0.01530.4451-0.16240.04230.01030.01860.1291-0.05540.0415-9.04931.1444-22.0285
Refinement TLS groupSelection: ALL

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