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- PDB-1lv9: CXCR3 Binding Chemokine IP-10/CXCL10 -

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Basic information

Entry
Database: PDB / ID: 1lv9
TitleCXCR3 Binding Chemokine IP-10/CXCL10
ComponentsSmall inducible cytokine B10
KeywordsCYTOKINE / chemokine
Function / homology
Function and homology information


regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / negative regulation of myoblast differentiation / T cell chemotaxis ...regulation of T cell chemotaxis / negative regulation of myoblast fusion / CXCR3 chemokine receptor binding / regulation of endothelial tube morphogenesis / cellular response to interleukin-17 / CXCR chemokine receptor binding / response to auditory stimulus / cAMP-dependent protein kinase regulator activity / negative regulation of myoblast differentiation / T cell chemotaxis / response to vitamin D / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / blood circulation / Chemokine receptors bind chemokines / endothelial cell activation / chemokine activity / muscle organ development / chemoattractant activity / Interleukin-10 signaling / antiviral innate immune response / positive regulation of T cell migration / negative regulation of angiogenesis / neutrophil chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / response to gamma radiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to virus / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / cell-cell signaling / heparin binding / cellular response to heat / regulation of cell population proliferation / G alpha (i) signalling events / cellular response to lipopolysaccharide / regulation of apoptotic process / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / external side of plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 ...CXC chemokine / CXC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-x-C subfamily signature. / CXC Chemokine domain / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
C-X-C motif chemokine 10
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsBooth, V. / Keizer, D.W. / Kamphuis, M.B. / Clark-Lewis, I. / Sykes, B.D.
CitationJournal: Biochemistry / Year: 2002
Title: The CXCR3 binding chemokine IP-10/CXCL10: structure and receptor interactions.
Authors: Booth, V. / Keizer, D.W. / Kamphuis, M.B. / Clark-Lewis, I. / Sykes, B.D.
History
DepositionMay 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Small inducible cytokine B10


Theoretical massNumber of molelcules
Total (without water)8,6511
Polymers8,6511
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Small inducible cytokine B10 / CXCL10 / Interferon-gamma induced protein / Gamma-IP10 / IP-10


Mass: 8651.370 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence of the protein is naturally found in Homo sapiens. It was synthesized by stepwise solid phase methods using t-butoxycarbonyl protection chemistry.
References: UniProt: P02778

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY

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Sample preparation

DetailsContents: 2 mM NMeLeu 27 IP-10 (no isotope labelling), 1 mM sodium azide, 1 mM DSS, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 5.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio et alprocessing
NMRView4.1.2Johnsondata analysis
X-PLOR3.851Brungerrefinement
ARIA1999Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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