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- PDB-3ink: UNRAVELING THE STRUCTURE OF INTERLEUKIN-2: REPLY -

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Basic information

Entry
Database: PDB / ID: 3ink
TitleUNRAVELING THE STRUCTURE OF INTERLEUKIN-2: REPLY
ComponentsINTERLEUKIN-2
KeywordsCYTOKINE
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 interleukin-17 production / positive regulation of activated T cell proliferation / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMckay, D.B. / Brandhuber, B.J.
Citation
#1: Journal: Science / Year: 1987
Title: Three-Dimensional Structure of Interleukin-2
Authors: Brandhuber, B.J. / Boone, T. / Kenney, W.C. / Mckay, D.B.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Crystals and a Low Resolution Structure of Interleukin-2
Authors: Brandhuber, B.J. / Boone, T. / Kenney, W.C. / Mckay, D.B.
#3: Journal: Science / Year: 1987
Title: Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design
Authors: Hardy, L.W. / Finer-Moore, J.S. / Montfort, W.R. / Jones, M.O. / Santi, D.V. / Stroud, R.M.
History
DepositionDec 9, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 4, 2013Group: Database references
Revision 1.4Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: INTERLEUKIN-2
D: INTERLEUKIN-2


Theoretical massNumber of molelcules
Total (without water)30,8082
Polymers30,8082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.800, 40.100, 33.700
Angle α, β, γ (deg.)90.00, 109.30, 93.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein INTERLEUKIN-2


Mass: 15403.915 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P60568
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.64 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.202 / Rfactor obs: 0.202 / Details: THE OVERALL B-FACTOR FOR THIS STRUCTURE IS 14.8.
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 0 1996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Rfactor obs: 0.202 / Num. reflection obs: 7275
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.8 Å2
Refine LS restraints
*PLUS
Type: x_angle_d

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