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- PDB-1m49: Crystal Structure of Human Interleukin-2 Complexed with SP-1985 -

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Basic information

Entry
Database: PDB / ID: 1m49
TitleCrystal Structure of Human Interleukin-2 Complexed with SP-1985
Componentsinterleukin-2
KeywordsCYTOKINE / four-helix bundle / small molecule complex
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / natural killer cell activation / protein kinase C-activating G protein-coupled receptor signaling pathway / positive regulation of regulatory T cell differentiation / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / adaptive immune response / transcription by RNA polymerase II / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CMM / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. ...Arkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Binding of small molecules to an adaptive protein-protein interface
Authors: Arkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: interleukin-2
B: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9954
Polymers30,8722
Non-polymers1,1232
Water1,874104
1
A: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9982
Polymers15,4361
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9982
Polymers15,4361
Non-polymers5621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.323, 58.379, 93.507
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 interleukin-2 / IL-2 / T-CELL GROWTH FACTOR / TCGF / ALDESLEUKIN


Mass: 15435.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60568
#2: Chemical ChemComp-CMM / 2-[2-(1-CARBAMIMIDOYL-PIPERIDIN-3-YL)-ACETYLAMINO]-3-{4-[2-(3-OXALYL-1H-INDOL-7-YL)ETHYL]-PHENYL}-PROPIONIC ACID METHYL ESTER


Mass: 561.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H35N5O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 16, 2000 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→10 Å / Num. all: 19589 / Num. obs: 19589 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 7.7 / Num. unique all: 1778 / Rsym value: 0.228 / % possible all: 92.8

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Processing

Software
NameClassification
d*TREKdata reduction
AMoREphasing
REFMACrefinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / SU B: 2.65307 / SU ML: 0.0754 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24266 / ESU R Free: 0.21094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27841 866 5 %RANDOM
Rwork0.22285 ---
all0.22556 16549 --
obs0.22556 16549 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 38.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--0.94 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 82 104 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0060.022
X-RAY DIFFRACTIONp_angle_deg1.2542.032
X-RAY DIFFRACTIONp_chiral_restr0.0740.2
X-RAY DIFFRACTIONp_plane_restr0.0030.02
X-RAY DIFFRACTIONp_mcbond_it2.0832.5
X-RAY DIFFRACTIONp_mcangle_it4.8735
X-RAY DIFFRACTIONp_scbond_it3.2232.5
X-RAY DIFFRACTIONp_scangle_it5.135
LS refinement shellResolution: 2→2.067 Å
RfactorNum. reflection% reflection
Rfree0.328 82 -
Rwork0.268 --
obs-1700 92.8 %

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