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- PDB-7aym: Structure of DDR2 Kinase domain in complex with IBZ3 -

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Basic information

Entry
Database: PDB / ID: 7aym
TitleStructure of DDR2 Kinase domain in complex with IBZ3
ComponentsDiscoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1
KeywordsMEMBRANE PROTEIN / Kinase / Receptor Tyrosine kinase Discoidin domain-containing receptor 2 / collagen / signal transduction / cell communication
Function / homology
Function and homology information


positive regulation of hepatic stellate cell proliferation / smooth muscle cell-matrix adhesion / 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 / regulation of cell-matrix adhesion / ear development ...positive regulation of hepatic stellate cell proliferation / smooth muscle cell-matrix adhesion / 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 / regulation of cell-matrix adhesion / ear development / 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 / branching involved in mammary gland duct morphogenesis / regulation of tissue remodeling / positive regulation of fibroblast migration / wound healing, spreading of cells / neuron projection extension / smooth muscle cell migration / positive regulation of wound healing / axon development / Non-integrin membrane-ECM interactions / positive regulation of collagen biosynthetic process / cellular response to angiotensin / mammary gland alveolus development / positive regulation of protein kinase activity / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of osteoblast differentiation / peptidyl-tyrosine autophosphorylation / 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 / lactation / embryo implantation / ossification / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of DNA-binding transcription factor activity / regulation of cell growth / 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 / cell population proliferation / 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 / negative regulation of cell population proliferation / focal adhesion / negative regulation of apoptotic process / signal transduction / extracellular space / extracellular exosome / ATP binding / metal ion 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-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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4VD / Epithelial discoidin domain-containing receptor 1 / Discoidin domain-containing receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsNawrotek, A. / Talagas, A. / Vuillard, L.M. / Miallau, L.
CitationJournal: To Be Published
Title: Structure of DDR2 Kinase domain in complex with IBZ3
Authors: Nawrotek, A. / Talagas, A. / Vuillard, L.M. / Miallau, L.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0452
Polymers38,6281
Non-polymers4171
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.75, 85.355, 89.541
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Discoidin domain-containing receptor 2,Epithelial discoidin domain-containing receptor 1 / Discoidin domain receptor 2 / CD167 antigen-like family member B / Discoidin domain-containing ...Discoidin domain receptor 2 / CD167 antigen-like family member B / Discoidin domain-containing receptor tyrosine kinase 2 / Neurotrophic tyrosine kinase / receptor-related 3 / Receptor protein-tyrosine kinase TKT / Tyrosine-protein kinase TYRO10 / Epithelial discoidin domain receptor 1 / CD167 antigen-like family member A / Cell adhesion kinase / Discoidin receptor tyrosine kinase / HGK2 / Mammary carcinoma kinase 10 / MCK-10 / Protein-tyrosine kinase 3A / Protein-tyrosine kinase RTK-6 / TRK E / Tyrosine kinase DDR / Tyrosine-protein kinase CAK /


Mass: 38627.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: DDR2, NTRKR3, TKT, TYRO10, DDR1, CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE
Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16832, UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-4VD / N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide


Mass: 417.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C23H20FN5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2 M tri-sodium citrate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980119 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980119 Å / Relative weight: 1
ReflectionResolution: 2.09→61.78 Å / Num. obs: 9068 / % possible obs: 88.6 % / Redundancy: 6.5 % / CC1/2: 0.988 / Net I/σ(I): 6
Reflection shellResolution: 2.09→2.436 Å / Num. unique obs: 453 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BKJ

4bkj


Resolution: 2.12→61.78 Å / Cor.coef. Fo:Fc: 0.856 / Cor.coef. Fo:Fc free: 0.781 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.383
RfactorNum. reflection% reflectionSelection details
Rfree0.289 515 -RANDOM
Rwork0.236 ---
obs0.239 9068 57 %-
Displacement parametersBiso mean: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.1514 Å20 Å20 Å2
2---2.0349 Å20 Å2
3----0.1166 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 2.12→61.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 31 8 2268

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