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- PDB-1m48: Crystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Amino... -

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Basic information

Entry
Database: PDB / ID: 1m48
TitleCrystal Structure of Human IL-2 Complexed with (R)-N-[2-[1-(Aminoiminomethyl)-3-piperidinyl]-1-oxoethyl]-4-(phenylethynyl)-L-phenylalanine methyl ester
Componentsinterleukin-2
KeywordsCYTOKINE / interleukin-2 / four-helix bundle / small molecule complex
Function / homology
Function and homology information


response to tacrolimus / kappa-type opioid receptor binding / interleukin-2 receptor binding / interleukin-2 receptor complex / glycosphingolipid binding / positive regulation of plasma cell differentiation / positive regulation of leukocyte differentiation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) ...response to tacrolimus / kappa-type opioid receptor binding / interleukin-2 receptor binding / interleukin-2 receptor complex / glycosphingolipid binding / positive regulation of plasma cell differentiation / positive regulation of leukocyte differentiation / 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 / interleukin-2-mediated signaling pathway / positive regulation of leukocyte proliferation / natural killer cell activation / Interleukin-2 signaling / cell surface receptor signaling pathway via STAT / negative regulation of B cell apoptotic process / positive regulation of activated T cell proliferation / kinase activator activity / positive regulation of interleukin-17 production / positive regulation of regulatory T cell differentiation / positive regulation of dendritic spine development / positive regulation of immunoglobulin production / T cell differentiation / positive regulation of B cell proliferation / Interleukin receptor SHC signaling / cell surface receptor signaling pathway via JAK-STAT / cytokine activity / growth factor activity / positive regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / cell-cell signaling / carbohydrate binding / positive regulation of cell growth / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / cell adhesion / response to ethanol / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / 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-FRG / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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
Revision 1.4Oct 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: interleukin-2
B: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7654
Polymers30,8722
Non-polymers8932
Water3,855214
1
A: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8832
Polymers15,4361
Non-polymers4471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8832
Polymers15,4361
Non-polymers4471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.470, 58.020, 93.080
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-FRG / 2-[3-METHYL-4-(N-METHYL-GUANIDINO)-BUTYRYLAMINO]-3-(4-PHENYLETHYNYL-PHENYL)-PROPIONIC ACID METHYL ESTER / (R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER


Mass: 446.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
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
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 23, 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: 1.95→10 Å / Num. all: 20214 / Num. obs: 20214 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.65 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 11.4
Reflection shellResolution: 1.95→2.016 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1846 / Rsym value: 0.357 / % possible all: 94.3

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Processing

Software
NameVersionClassification
d*TREKdata reduction
AMoREphasing
REFMAC5.1.19refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26891 974 4.9 %RANDOM
Rwork0.19716 ---
all0.20046 19081 --
obs0.20046 19081 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 66 214 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222125
X-RAY DIFFRACTIONr_angle_refined_deg1.4222.0162864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7785245
X-RAY DIFFRACTIONr_chiral_restr0.1210.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021501
X-RAY DIFFRACTIONr_nbd_refined0.220.21082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2121
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.220
X-RAY DIFFRACTIONr_mcbond_it3.2592.51244
X-RAY DIFFRACTIONr_mcangle_it5.02752030
X-RAY DIFFRACTIONr_scbond_it3.7442.5881
X-RAY DIFFRACTIONr_scangle_it5.3545834
LS refinement shellResolution: 1.95→2.016 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.389 95 -
Rwork0.303 1751 -
obs-1846 94.3 %

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