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- PDB-2z4f: Solution structure of the Discoidin Domain of DDR2 -

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Basic information

Entry
Database: PDB / ID: 2z4f
TitleSolution structure of the Discoidin Domain of DDR2
ComponentsDiscoidin domain-containing receptor 2
KeywordsTRANSFERASE / BETA BARREL
Function / homology
Function and homology information


positive regulation of hepatic stellate cell proliferation / biomineral tissue development / positive regulation of hepatic stellate cell activation / chondrocyte proliferation / positive regulation of extracellular matrix disassembly / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization ...positive regulation of hepatic stellate cell proliferation / biomineral tissue development / positive regulation of hepatic stellate cell activation / chondrocyte proliferation / positive regulation of extracellular matrix disassembly / endochondral bone growth / regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / regulation of tissue remodeling / positive regulation of fibroblast migration / positive regulation of wound healing / Non-integrin membrane-ECM interactions / positive regulation of collagen biosynthetic process / cellular response to angiotensin / positive regulation of protein kinase activity / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / collagen binding / positive regulation of vascular associated smooth muscle cell proliferation / response to muscle stretch / transmembrane receptor protein tyrosine kinase activity / ossification / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of DNA-binding transcription factor activity / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / positive regulation of fibroblast proliferation / actin cytoskeleton / protein autophosphorylation / cellular response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / signal transduction / ATP binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Galactose-binding domain-like / : / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Discoidin domain-containing receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIchikawa, O. / Osawa, M. / Nishida, N. / Goshima, N. / Nomura, N. / Shimada, I.
CitationJournal: Embo J. / Year: 2007
Title: Structural basis of the collagen-binding mode of discoidin domain receptor 2
Authors: Ichikawa, O. / Osawa, M. / Nishida, N. / Goshima, N. / Nomura, N. / Shimada, I.
History
DepositionJun 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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:
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Assembly

Deposited unit
A: Discoidin domain-containing receptor 2


Theoretical massNumber of molelcules
Total (without water)19,3941
Polymers19,3941
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)20 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Discoidin domain-containing receptor 2 / Discoidin domain receptor 2 / Receptor protein-tyrosine kinase TKT / Tyrosine-protein kinase TYRO10 ...Discoidin domain receptor 2 / Receptor protein-tyrosine kinase TKT / Tyrosine-protein kinase TYRO10 / Neurotrophic tyrosine kinase / receptor-related 3 / CD167b antigen


Mass: 19393.707 Da / Num. of mol.: 1 / Fragment: F5/8 type C, DISCOIDIN DOMAIN, RESIDUES 26-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDR2 / Production host: Pichia pastoris (fungus)
References: UniProt: Q16832, receptor protein-tyrosine kinase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
131HNHA
1423D 13C-separated NOESY
1533D 15N-separated NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM DDR2 U-15N,13C; 10mM PHOSPHATE BUFFER; 100mM NACL; 95% H2O, 5% D2O95% H2O/5% D2O
20.4mM DDR2 U-15N,13C; 10mM PHOSPHATE BUFFER; 100mM NACL; 100% D2O100% D2O
30.4mM DDR2 U-15N; 10mM PHOSPHATE BUFFER; 100mM NACL; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 0.1M / pH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1GUNTERT, P. ET AL.refinement
CYANA2.1GUNTERT, P. ET AL.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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