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- PDB-1mkc: C-TERMINAL DOMAIN OF MIDKINE -

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Basic information

Entry
Database: PDB / ID: 1mkc
TitleC-TERMINAL DOMAIN OF MIDKINE
ComponentsPROTEIN (MIDKINE)
KeywordsHEPARIN-BINDING GROWTH FACTOR
Function / homology
Function and homology information


defecation / cerebellar granular layer development / positive regulation of inflammatory response to wounding / positive regulation of neutrophil extravasation / regulation of chondrocyte differentiation / glial cell projection elongation / positive regulation of artery morphogenesis / positive regulation of smooth muscle cell chemotaxis / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding ...defecation / cerebellar granular layer development / positive regulation of inflammatory response to wounding / positive regulation of neutrophil extravasation / regulation of chondrocyte differentiation / glial cell projection elongation / positive regulation of artery morphogenesis / positive regulation of smooth muscle cell chemotaxis / leukocyte chemotaxis involved in inflammatory response / chondroitin sulfate binding / positive regulation of leukocyte cell-cell adhesion / positive regulation of keratinocyte proliferation / regulation of bone remodeling / positive regulation of cartilage development / negative regulation of inflammatory response to wounding / regulation of behavior / MDK and PTN in ALK signaling / negative regulation of regulatory T cell differentiation / T cell activation involved in immune response / response to auditory stimulus / positive regulation of blood vessel branching / tissue regeneration / positive regulation of neuron migration / short-term memory / negative regulation of epithelial cell apoptotic process / dentate gyrus development / positive regulation of neural precursor cell proliferation / heparan sulfate binding / negative regulation of cell adhesion / negative regulation of ossification / positive regulation of neutrophil chemotaxis / positive regulation of hepatocyte proliferation / positive regulation of leukocyte chemotaxis / positive regulation of T cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / adrenal gland development / Signaling by ALK / positive regulation of oligodendrocyte differentiation / oogenesis / positive regulation of macrophage chemotaxis / positive regulation of cell division / positive regulation of cell adhesion / estrous cycle / behavioral fear response / positive regulation of epithelial to mesenchymal transition / positive regulation of substrate adhesion-dependent cell spreading / cytoskeleton organization / NOTCH2 Activation and Transmission of Signal to the Nucleus / positive regulation of interleukin-12 production / growth factor activity / negative regulation of canonical Wnt signaling pathway / cerebral cortex development / positive regulation of neuron projection development / response to wounding / positive regulation of inflammatory response / nervous system development / heparin binding / negative regulation of neuron apoptotic process / cell differentiation / intracellular signal transduction / positive regulation of cell migration / positive regulation of DNA-templated transcription / signal transduction / extracellular region
Similarity search - Function
Heparin-binding Growth Factor, Midkine; Chain A, C-terminal Domain; / Heparin-binding Growth Factor, Midkine; Chain A- C-terminal Domain / Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily ...Heparin-binding Growth Factor, Midkine; Chain A, C-terminal Domain; / Heparin-binding Growth Factor, Midkine; Chain A- C-terminal Domain / Pleiotrophin/Midkine heparin-binding growth factor, conserved site / PTN/MK heparin-binding protein family signature 1. / PTN/MK heparin-binding protein family signature 2. / Midkine heparin-binding growth factor / Pleiotrophin/Midkine, N-terminal domain / Pleiotrophin/Midkine, C-terminal domain / Pleiotrophin/Midkine disulphide-rich domain superfamily / Pleiotrophin/Midkine, N-terminal domain superfamily / Pleiotrophin/Midkine, C-terminal domain superfamily / PTN/MK heparin-binding protein family, C-terminal domain / PTN/MK heparin-binding protein family, N-terminal domain / Pleiotrophin / midkine family / Roll / Mainly Beta
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry
AuthorsIwasaki, W. / Nagata, K. / Hatanaka, H. / Ogura, K. / Inui, T. / Kimura, T. / Muramatsu, T. / Yoshida, K. / Tasumi, M. / Inagaki, F.
CitationJournal: EMBO J. / Year: 1997
Title: Solution structure of midkine, a new heparin-binding growth factor.
Authors: Iwasaki, W. / Nagata, K. / Hatanaka, H. / Inui, T. / Kimura, T. / Muramatsu, T. / Yoshida, K. / Tasumi, M. / Inagaki, F.
History
DepositionMar 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (MIDKINE)


Theoretical massNumber of molelcules
Total (without water)4,8491
Polymers4,8491
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)1 / -
Representative

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Components

#1: Protein/peptide PROTEIN (MIDKINE)


Mass: 4848.589 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Source method: obtained synthetically
Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: P21741

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
NMR detailsText: MEAN STRUCTURE.

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionspH: 5.0 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS 600 / Manufacturer: Varian / Model: UNITYPLUS 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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