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- PDB-1qvn: Structure of SP4160 Bound to IL-2 V69A -

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Basic information

Entry
Database: PDB / ID: 1qvn
TitleStructure of SP4160 Bound to IL-2 V69A
ComponentsInterleukin-2
KeywordsCYTOKINE / IL-2 Small Molecule hot spot
Function / homology
Function and homology information


kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / 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 / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / kinase activator activity / natural killer cell activation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / 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 / extrinsic apoptotic signaling pathway in absence of ligand / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / RAF/MAP kinase cascade / positive regulation of cell growth / response to ethanol / phospholipase C-activating G protein-coupled receptor signaling pathway / 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
2-GUANIDINO-4-METHYL-PENTANOIC ACID / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsThanos, C.D. / Delano, W.L. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Hot-spot mimicry of a cytokine receptor by a small molecule.
Authors: Thanos, C.D. / DeLano, W.L. / Wells, J.A.
History
DepositionAug 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)64,23212
Polymers61,2274
Non-polymers3,0048
Water00
1
A: Interleukin-2
C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1166
Polymers30,6142
Non-polymers1,5024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interleukin-2
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1166
Polymers30,6142
Non-polymers1,5024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-90 kcal/mol
Surface area13890 Å2
MethodPISA
3
A: Interleukin-2
hetero molecules

C: Interleukin-2
hetero molecules

B: Interleukin-2
D: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,23212
Polymers61,2274
Non-polymers3,0048
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_654-x+3/2,-y,z-1/21
crystal symmetry operation2_554-x+1/2,-y,z-1/21
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-186 kcal/mol
Surface area26860 Å2
MethodPISA
4
A: Interleukin-2
hetero molecules

C: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1166
Polymers30,6142
Non-polymers1,5024
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3260 Å2
ΔGint-93 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.514, 85.134, 122.141
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: 15306.823 Da / Num. of mol.: 4 / Mutation: V69A
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FRI / 2-GUANIDINO-4-METHYL-PENTANOIC ACID [2-(4-{5-[4-(4-ACETYLAMINO-BENZYLOXY)-2,3-DICHLORO-PHENYL]-2-METHYL-2H-PYRAZOL-3-YL}-PIPERIDIN-1-YL)-2-OXO-ETHYL]-AMIDE / SP4160


Mass: 685.644 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H42Cl2N8O4
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: 2.27 Å3/Da / Density % sol: 45.86 %
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

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 24, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 14582 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.768 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.86 / SU B: 18.871 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30784 771 5 %RANDOM
Rwork0.25844 ---
all0.26098 40387 --
obs0.26098 14582 97.1 %-
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: 19.777 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å20 Å2
2--3.41 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 0 192 0 4108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d1.8880.0224130
X-RAY DIFFRACTIONr_angle_refined_deg14.7892.0245569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4365480
X-RAY DIFFRACTIONr_chiral_restr7.0590.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0690.022948
X-RAY DIFFRACTIONr_gen_planes_other0.4710.024
X-RAY DIFFRACTIONr_nbd_refined0.6580.22264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.25
X-RAY DIFFRACTIONr_mcbond_it1.2962.52448
X-RAY DIFFRACTIONr_mcangle_it2.38353967
X-RAY DIFFRACTIONr_scbond_it4.5062.51682
X-RAY DIFFRACTIONr_scangle_it4.89151602
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.449 54
Rwork0.295 1036
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)
17.16970.34941.45820.81320.3191.98660.0595-0.003-0.1514-0.0633-0.00970.04210.2319-0.1754-0.04990.5165-0.0394-0.01550.39190.0010.444533.132215.407285.9276
22.7124-1.2627-0.741.3139-0.03711.05330.1474-0.07930.2831-0.00360.0366-0.0002-0.19480.1255-0.1840.4356-0.01580.00910.4335-0.00590.469239.765623.17159.2933
33.8009-1.689-0.13492.61240.2991.0658-0.0333-0.01460.1962-0.1021-0.0095-0.0538-0.1197-0.10590.04280.4486-0.0193-0.00460.44280.01130.38340.21325.548869.4215
42.5673-1.56770.56331.4162-0.70131.7450.01520.0664-0.12140.0046-0.04250.1060.10410.21660.02720.4661-0.00870.02190.4312-0.01060.434919.05898.873922.1264
57.6531-16.0323-1.513-4.022926.4964-11.04530.1081-0.35830.8265-0.5663-1.399-0.6514-2.9061.02071.29080.7471-0.1136-0.09080.7563-0.05270.882916.42816.981480.4671
619.05180.53523.768254.205912.949911.48640.082-0.2239-1.101-1.13340.0509-3.71470.50780.3231-0.13290.4027-0.0229-0.02590.4411-0.03850.441251.287813.68780.2049
711.06152.0928-3.7663-14.838322.52723.9421-0.04970.2561-0.8059-0.1313-0.3984-1.00321.44141.46610.44810.47720.0711-0.02530.5577-0.00670.395311.484113.698563.5567
85.4964-4.0689-6.6832-27.056425.26243.95280.0547-0.2341-0.5205-1.2186-0.10440.8647-0.6448-1.23760.04970.5739-0.1011-0.07220.8223-0.14010.60382.038911.928217.7677
90000000000000001.01760.1192-0.05450.54930.51391.064129.574514.364811.6986
100000000000000001.24160.1635-0.56730.47990.0660.669441.710717.868775.4306
110000000000000000.71170.04540.34530.30060.01330.601448.033817.3557-5.8098
120000000000000000.50160.10790.17920.4580.17540.74128.690116.023756.5732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1324 - 132
2X-RAY DIFFRACTION2BB4 - 1324 - 132
3X-RAY DIFFRACTION3CC4 - 1324 - 132
4X-RAY DIFFRACTION4DD4 - 1324 - 132
5X-RAY DIFFRACTION5AI2011
6X-RAY DIFFRACTION6BJ3011
7X-RAY DIFFRACTION7CK4011
8X-RAY DIFFRACTION8DL5011
9X-RAY DIFFRACTION9BE6011
10X-RAY DIFFRACTION10AF7011
11X-RAY DIFFRACTION11BG8011
12X-RAY DIFFRACTION12CH9011

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