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- PDB-1py2: Structure of a 60 nM Small Molecule Bound to a Hot Spot on IL-2 -

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Basic information

Entry
Database: PDB / ID: 1py2
TitleStructure of a 60 nM Small Molecule Bound to a Hot Spot on IL-2
ComponentsInterleukin-2
KeywordsIMMUNE SYSTEM / IL-2 / interleukin 2 / small molecule / hot spot / molecular recognition
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling ...kappa-type opioid receptor binding / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / response to tacrolimus / positive regulation of plasma cell differentiation / glycosphingolipid binding / negative regulation of lymphocyte proliferation / negative regulation of T-helper 17 cell differentiation / positive regulation of tissue remodeling / 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 / kinase activator activity / positive regulation of regulatory T cell differentiation / natural killer cell activation / : / 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 / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of B cell proliferation / 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-FRH / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsThanos, C.D. / Randal, M. / Wells, J.A.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Potent small-molecule binding to a dynamic hot spot on IL-2.
Authors: Thanos, C.D. / Randal, M. / Wells, J.A.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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
C: Interleukin-2
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,18611
Polymers61,3404
Non-polymers2,8467
Water00
1
A: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9972
Polymers15,3351
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1284
Polymers15,3351
Non-polymers7933
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0633
Polymers15,3351
Non-polymers7282
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9972
Polymers15,3351
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0633
Polymers15,3351
Non-polymers7282
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
B: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1284
Polymers15,3351
Non-polymers7933
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.982, 52.448, 89.469
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Interleukin-2 / IL-2 / T-cell growth factor / TCGF / Aldesleukin


Mass: 15334.876 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60568
#2: Chemical
ChemComp-FRH / 5-[2,3-DICHLORO-4-(5-{1-[2-(2-GUANIDINO-4-METHYL-PENTANOYLAMINO)-ACETYL]-PIPERIDIN-4-YL}-1-METHYL-1H-PYRAZOL-3-YL)-PHENOXYMETHYL]-FURAN-2-CARBOXYLIC ACID


Mass: 662.564 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H37Cl2N7O6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.05 M Zinc Acetate, 0.075 M Magnesium Chloride, 18% (w/v) Polyethylene Glycol 10K, 0.1M Sodium Cacodylate, pH 5.9. , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.05 Mzinc acetate1reservoir
20.075 M1reservoirMgCl2
318 %(w/v)PEG100001reservoir
40.1 Msodium cacodylate1reservoirpH5.9

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorDetector: CCD / Date: Jan 24, 2003
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. all: 13660 / Num. obs: 15034 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.91 Å / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 12442 / % possible obs: 97.4 % / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.83 / SU B: 22.885 / SU ML: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31961 640 4.9 %RANDOM
Rwork0.27105 ---
all0.273 13660 --
obs0.27343 12442 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.459 Å2
Baniso -1Baniso -2Baniso -3
1-3.84 Å20 Å23.67 Å2
2---2.69 Å20 Å2
3---0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 183 0 4015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223891
X-RAY DIFFRACTIONr_angle_refined_deg1.2332.0345282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5565453
X-RAY DIFFRACTIONr_chiral_restr0.0420.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.022816
X-RAY DIFFRACTIONr_nbd_refined0.1410.21605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.26
X-RAY DIFFRACTIONr_mcbond_it0.8262.52328
X-RAY DIFFRACTIONr_mcangle_it1.50453734
X-RAY DIFFRACTIONr_scbond_it0.6852.51563
X-RAY DIFFRACTIONr_scangle_it1.16451548
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.394 40
Rwork0.34 891
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.97130.9354-0.10344.48980.63984.15510.0899-0.00740.06130.2091-0.1130.4118-0.11-0.05540.0230.23540.00510.03770.27090.01670.380521.20370.41493.5042
21.83522.0791-0.15365.03570.32623.1125-0.04230.0830.1190.03010.11430.24290.0115-0.2705-0.0720.30870.0845-0.08770.3954-0.01920.293740.506139.447749.2625
32.27610.4284-2.38544.8402-1.74314.87150.09350.096-0.05130.21820.02020.2541-0.0685-0.3175-0.11360.2131-0.0320.00560.417-0.06080.378218.80665.344763.6622
40.8009-0.23760.31986.69073.45553.0796-0.0287-0.0801-0.04340.1366-0.24270.1782-0.1411-0.25030.27140.33360.0518-0.01910.46750.00210.2756-18.860317.870667.4941
59.6181-16.6677-1.2124-2.3279-16.044851.89420.2803-0.28240.32311.76140.2044-0.0621-1.45661.0697-0.48460.5317-0.2762-0.08490.2658-0.05190.55133.932611.44036.3478
648.0875-9.770332.53836.59020.213126.67690.7374-0.328-0.00290.47580.8077-1.9792-0.77790.3444-1.54510.4356-0.30130.00090.42320.02020.566753.922149.466547.8267
717.0267-15.31450.513811.7356-40.779660.3147-1.6975-2.5563-2.6549-0.90230.1819-0.05634.403-1.13961.51551.1887-0.2430.25660.66430.20151.290517.2698-11.533867.0197
827.449-19.590415.5985-11.153916.827832.9381-0.1891.6892-2.541-0.2509-1.02751.3713-0.54451.16891.21650.6-0.07580.20750.4455-0.06990.7374-16.18122.175762.6147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1326 - 132
2X-RAY DIFFRACTION2BB6 - 1326 - 132
3X-RAY DIFFRACTION3CC7 - 1317 - 131
4X-RAY DIFFRACTION4DD6 - 1326 - 132
5X-RAY DIFFRACTION5AH2011
6X-RAY DIFFRACTION6BI3011
7X-RAY DIFFRACTION7CJ4011
8X-RAY DIFFRACTION8DK5011
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.273
Solvent computation
*PLUS
Displacement parameters
*PLUS

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