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- PDB-5ews: Sugar binding protein - human galectin-2 -

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Basic information

Entry
Database: PDB / ID: 5ews
TitleSugar binding protein - human galectin-2
ComponentsGalectin-2
KeywordsSUGAR BINDING PROTEIN / lactose / galectin
Function / homology
Function and homology information


galectin complex / galactoside binding / T cell homeostasis / cell-cell adhesion / positive regulation of inflammatory response / carbohydrate binding / positive regulation of apoptotic process
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
beta-lactose / Galectin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSu, J.Y. / Si, Y.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500637 China
Drug Discovery Found of Jilin Province20150311057YY China
CitationJournal: Acta Biochim. Biophys. Sin. (Shanghai) / Year: 2016
Title: Human galectin-2 interacts with carbohydrates and peptides non-classically: new insight from X-ray crystallography and hemagglutination.
Authors: Si, Y. / Feng, S. / Gao, J. / Wang, Y. / Zhang, Z. / Meng, Y. / Zhou, Y. / Tai, G. / Su, J.
History
DepositionNov 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_atom_id / _struct_conn.ptnr1_label_comp_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Galectin-2
A: Galectin-2
C: Galectin-2
D: Galectin-2
E: Galectin-2
F: Galectin-2
G: Galectin-2
H: Galectin-2
I: Galectin-2
J: Galectin-2
K: Galectin-2
L: Galectin-2
M: Galectin-2
N: Galectin-2
O: Galectin-2
P: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,80424
Polymers237,06616
Non-polymers2,7388
Water7,656425
1
B: Galectin-2
N: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-4 kcal/mol
Surface area11390 Å2
MethodPISA
2
A: Galectin-2
M: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-1 kcal/mol
Surface area11400 Å2
MethodPISA
3
C: Galectin-2
K: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-1 kcal/mol
Surface area11940 Å2
MethodPISA
4
D: Galectin-2
L: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-1 kcal/mol
Surface area11590 Å2
MethodPISA
5
E: Galectin-2
H: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-0 kcal/mol
Surface area11400 Å2
MethodPISA
6
F: Galectin-2
G: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area11580 Å2
MethodPISA
7
I: Galectin-2
O: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-1 kcal/mol
Surface area11360 Å2
MethodPISA
8
J: Galectin-2
P: Galectin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,6332
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-3 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.401, 106.943, 121.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN AA1 - 134
211CHAIN BB1 - 134
311CHAIN CC1 - 134
411CHAIN DD1 - 134
511CHAIN EE1 - 134
611CHAIN FF1 - 134
711CHAIN GG1 - 134
811CHAIN HH1 - 134
911CHAIN II1 - 134
1011CHAIN JJ1 - 134
1111CHAIN KK1 - 134
1211CHAIN LL1 - 134
1311CHAIN MM1 - 134
1411CHAIN NN1 - 134
1511CHAIN OO1 - 134
1611CHAIN PP1 - 134

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Components

#1: Protein
Galectin-2 / Gal-2 / Beta-galactoside-binding lectin L-14-II / HL14 / Lactose-binding lectin 2 / S-Lac lectin 2


Mass: 14816.615 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P05162
#2: Polysaccharide
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 2→48.95 Å / Num. obs: 127534 / % possible obs: 97.6 % / Redundancy: 3.5 % / Net I/σ(I): 7.7

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155 / Classification: refinement
RefinementResolution: 2→48.946 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.04 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2493 2027 1.59 %
Rwork0.2137 --
obs0.2145 127532 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.97 Å2 / Biso mean: 31.9803 Å2 / Biso min: 11.61 Å2
Refinement stepCycle: final / Resolution: 2→48.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16264 0 184 425 16873
Biso mean--37.54 34.33 -
Num. residues----2096
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7203X-RAY DIFFRACTION13.763TORSIONAL
12B7203X-RAY DIFFRACTION13.763TORSIONAL
13C7203X-RAY DIFFRACTION13.763TORSIONAL
14D7203X-RAY DIFFRACTION13.763TORSIONAL
15E7203X-RAY DIFFRACTION13.763TORSIONAL
16F7203X-RAY DIFFRACTION13.763TORSIONAL
17G7203X-RAY DIFFRACTION13.763TORSIONAL
18H7203X-RAY DIFFRACTION13.763TORSIONAL
19I7203X-RAY DIFFRACTION13.763TORSIONAL
110J7203X-RAY DIFFRACTION13.763TORSIONAL
111K7203X-RAY DIFFRACTION13.763TORSIONAL
112L7203X-RAY DIFFRACTION13.763TORSIONAL
113M7203X-RAY DIFFRACTION13.763TORSIONAL
114N7203X-RAY DIFFRACTION13.763TORSIONAL
115O7203X-RAY DIFFRACTION13.763TORSIONAL
116P7203X-RAY DIFFRACTION13.763TORSIONAL

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