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- PDB-5h9q: Crystal Structure of Human Galectin-7 in Complex with TD139 -

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Basic information

Entry
Database: PDB / ID: 5h9q
TitleCrystal Structure of Human Galectin-7 in Complex with TD139
ComponentsGalectin-7
KeywordsSUGAR BINDING PROTEIN / galectin / thio-digalactoside (TD139) / pi-arginine interaction / fluorine bonding
Function / homology
Function and homology information


heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / apoptotic process / extracellular space / extracellular exosome / nucleus / 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-TD2 / Galectin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 Å
AuthorsHsieh, T.J. / Lin, H.Y. / Lin, C.H.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Lin, T.C. / Wu, S.C. / Tseng, Y.Y. / Liu, F.T. / Danny Hsu, S.T. / Lin, C.H.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-7
B: Galectin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9233
Polymers34,2742
Non-polymers6491
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint1 kcal/mol
Surface area12750 Å2
Unit cell
Length a, b, c (Å)53.896, 64.426, 70.616
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-7 / / Gal-7 / HKL-14 / PI7 / p53-induced gene 1 protein


Mass: 17137.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS7, PIG1, LGALS7B / Plasmid: pET28a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P47929
#2: Chemical ChemComp-TD2 / 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside


Mass: 648.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30F2N6O8S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.22 M Mg Acetate, 21% (w/v) PEG3350 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 19082 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 44.9
Reflection shellResolution: 1.93→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 11.86 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKZ

1bkz


Resolution: 1.931→27.651 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1892 10.02 %
Rwork0.189 --
obs0.194 18877 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.931→27.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 45 256 2404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052205
X-RAY DIFFRACTIONf_angle_d1.0012991
X-RAY DIFFRACTIONf_dihedral_angle_d22.757873
X-RAY DIFFRACTIONf_chiral_restr0.039307
X-RAY DIFFRACTIONf_plane_restr0.005402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9309-1.97920.25561270.18781143X-RAY DIFFRACTION96
1.9792-2.03270.26041340.18761183X-RAY DIFFRACTION98
2.0327-2.09250.24971320.1831170X-RAY DIFFRACTION99
2.0925-2.160.26131320.19661213X-RAY DIFFRACTION99
2.16-2.23720.24781320.20381179X-RAY DIFFRACTION99
2.2372-2.32670.27911340.211207X-RAY DIFFRACTION99
2.3267-2.43250.27981340.21011198X-RAY DIFFRACTION100
2.4325-2.56070.26381350.20561217X-RAY DIFFRACTION100
2.5607-2.7210.26591350.20421203X-RAY DIFFRACTION99
2.721-2.93090.2471350.21681216X-RAY DIFFRACTION100
2.9309-3.22540.24731370.19291238X-RAY DIFFRACTION100
3.2254-3.69120.19081380.17091240X-RAY DIFFRACTION100
3.6912-4.6470.20781390.15781252X-RAY DIFFRACTION100
4.647-27.65340.22861480.18891326X-RAY DIFFRACTION100

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