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- PDB-4q1r: Galectin-1 in Complex with Ligand AN027 -

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Basic information

Entry
Database: PDB / ID: 4q1r
TitleGalectin-1 in Complex with Ligand AN027
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / rational drug design
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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-2XU / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsGrimm, C. / Bertleff-Zieschang, N.
CitationJournal: To be Published
Title: Galectin-1 in Complex with Ligand AN027
Authors: Grimm, C. / Bertleff-Zieschang, N.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)31,4095
Polymers30,0322
Non-polymers1,3773
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6572
Polymers15,0161
Non-polymers6411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7533
Polymers15,0161
Non-polymers7372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.140, 58.410, 111.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 15016.079 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-2XU / propyl 2-(acetylamino)-2-deoxy-4-O-[3-O-({1-[2-(3-hydroxyphenyl)-2-oxoethyl]-1H-1,2,3-triazol-4-yl}methyl)-beta-D-galactopyranosyl]-beta-D-glucopyranoside


Mass: 640.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H40N4O13
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9764 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 1.47→51.707 Å / Num. obs: 48330 / % possible obs: 99.3 % / Rsym value: 0.047 / Net I/σ(I): 15.8
Reflection shellHighest resolution: 1.47 Å

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→51.707 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1939 2000 4.14 %
Rwork0.1545 --
obs0.1561 48324 99.29 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→51.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 95 206 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112374
X-RAY DIFFRACTIONf_angle_d1.5463246
X-RAY DIFFRACTIONf_dihedral_angle_d18.623899
X-RAY DIFFRACTIONf_chiral_restr0.078355
X-RAY DIFFRACTIONf_plane_restr0.007435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50670.33211410.26583278X-RAY DIFFRACTION99
1.5067-1.54750.26741400.22043250X-RAY DIFFRACTION99
1.5475-1.5930.27381400.19553224X-RAY DIFFRACTION98
1.593-1.64440.26111410.17793256X-RAY DIFFRACTION99
1.6444-1.70320.26331420.17733299X-RAY DIFFRACTION100
1.7032-1.77140.21641430.1713308X-RAY DIFFRACTION100
1.7714-1.8520.22481400.1553244X-RAY DIFFRACTION99
1.852-1.94970.1941420.13513300X-RAY DIFFRACTION99
1.9497-2.07180.16711430.12653322X-RAY DIFFRACTION100
2.0718-2.23180.17871430.12723287X-RAY DIFFRACTION100
2.2318-2.45640.19581430.13493319X-RAY DIFFRACTION99
2.4564-2.81180.18771450.14863361X-RAY DIFFRACTION100
2.8118-3.54250.19191450.15293363X-RAY DIFFRACTION99
3.5425-51.73930.16541520.16083513X-RAY DIFFRACTION99

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