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- PDB-4q1p: Galectin-1 in Complex with Ligand NB169 -

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Basic information

Entry
Database: PDB / ID: 4q1p
TitleGalectin-1 in Complex with Ligand NB169
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / rational drug design
Function / homology
Function and homology information


galectin complex / lactose binding / plasma cell differentiation / 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) ...galectin complex / lactose binding / plasma cell differentiation / 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) / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / 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 / cytosol / cytoplasm
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-2XT / BETA-MERCAPTOETHANOL / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsGrimm, C. / Bertleff-Zieschang, N.
CitationJournal: To be Published
Title: Galectin-1 in Complex with Ligand NB169
Authors: Grimm, C. / Bertleff-Zieschang, N.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: 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-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4006
Polymers30,0322
Non-polymers1,3674
Water4,035224
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)15,6913
Polymers15,0161
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7093
Polymers15,0161
Non-polymers6932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.267, 58.373, 111.066
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-2XT / propyl 2-(acetylamino)-4-O-{3-O-[(1-benzyl-1H-1,2,3-triazol-4-yl)methyl]-beta-D-galactopyranosyl}-2-deoxy-beta-D-glucopyranoside


Mass: 596.627 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H40N4O11
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M 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
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.46→55.533 Å / Num. all: 49698 / Num. obs: 49191 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 13 / Rsym value: 0.067
Reflection shellHighest resolution: 1.46 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: 1.46→40.316 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 2492 5.07 %
Rwork0.1491 --
obs0.1511 49185 98.97 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→40.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 93 224 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132345
X-RAY DIFFRACTIONf_angle_d1.5373194
X-RAY DIFFRACTIONf_dihedral_angle_d19.018889
X-RAY DIFFRACTIONf_chiral_restr0.08350
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.48810.33521290.2722550X-RAY DIFFRACTION99
1.4881-1.51850.39241330.2522529X-RAY DIFFRACTION99
1.5185-1.55150.30061260.22282564X-RAY DIFFRACTION98
1.5515-1.58760.2681410.1912508X-RAY DIFFRACTION98
1.5876-1.62730.26261430.17592550X-RAY DIFFRACTION99
1.6273-1.67130.26021370.17852583X-RAY DIFFRACTION99
1.6713-1.72050.23031620.16982550X-RAY DIFFRACTION99
1.7205-1.7760.23111460.16612580X-RAY DIFFRACTION100
1.776-1.83950.23941400.15692578X-RAY DIFFRACTION100
1.8395-1.91310.19411310.13942600X-RAY DIFFRACTION100
1.9131-2.00020.17441320.13162554X-RAY DIFFRACTION98
2.0002-2.10560.19441500.1222594X-RAY DIFFRACTION100
2.1056-2.23750.1391190.12532640X-RAY DIFFRACTION100
2.2375-2.41030.16611700.12742599X-RAY DIFFRACTION99
2.4103-2.65280.16461390.13872620X-RAY DIFFRACTION99
2.6528-3.03650.18011100.14472645X-RAY DIFFRACTION99
3.0365-3.82530.15311410.13812675X-RAY DIFFRACTION99
3.8253-40.33110.17151430.15412774X-RAY DIFFRACTION98

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