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- PDB-1fvr: TIE2 KINASE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1fvr
TitleTIE2 KINASE DOMAIN
ComponentsTYROSINE-PROTEIN KINASE TIE-2
KeywordsTRANSFERASE / tyrosine kinase
Function / homology
Function and homology information


Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / endochondral ossification / regulation of vascular permeability / heart trabecula formation / definitive hemopoiesis / endothelial cell proliferation / sprouting angiogenesis ...Tie signaling pathway / glomerulus vasculature development / regulation of establishment or maintenance of cell polarity / regulation of endothelial cell apoptotic process / endochondral ossification / regulation of vascular permeability / heart trabecula formation / definitive hemopoiesis / endothelial cell proliferation / sprouting angiogenesis / positive regulation of Rho protein signal transduction / growth factor binding / positive regulation of Rac protein signal transduction / positive regulation of intracellular signal transduction / microvillus / positive regulation of focal adhesion assembly / negative regulation of endothelial cell apoptotic process / response to cAMP / Tie2 Signaling / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of angiogenesis / basal plasma membrane / 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 / negative regulation of inflammatory response / response to estrogen / cellular response to mechanical stimulus / positive regulation of angiogenesis / cell-cell junction / cell-cell signaling / signaling receptor activity / heart development / RAF/MAP kinase cascade / basolateral plasma membrane / angiogenesis / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of MAPK cascade / ciliary basal body / apical plasma membrane / membrane raft / focal adhesion / centrosome / negative regulation of apoptotic process / cell surface / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / : / EGF-like domain signature 2. / EGF-like domain ...Tyrosine-protein kinase, receptor Tie-2, Ig-like domain 1, N-terminal / Tie-2 Ig-like domain 1 / Laminin-type EGF domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / : / EGF-like domain signature 2. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III 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 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Angiopoietin-1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsShewchuk, L.M. / Hassell, A.M. / Ellis, B. / Holmes, W.D. / Davis, R. / Horne, E.L. / Kadwell, S.H. / McKee, D.D. / Moore, J.T.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure of the Tie2 RTK domain: self-inhibition by the nucleotide binding loop, activation loop, and C-terminal tail.
Authors: Shewchuk, L.M. / Hassell, A.M. / Ellis, B. / Holmes, W.D. / Davis, R. / Horne, E.L. / Kadwell, S.H. / McKee, D.D. / Moore, J.T.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TYROSINE-PROTEIN KINASE TIE-2
B: TYROSINE-PROTEIN KINASE TIE-2


Theoretical massNumber of molelcules
Total (without water)75,0582
Polymers75,0582
Non-polymers00
Water7,945441
1
A: TYROSINE-PROTEIN KINASE TIE-2


Theoretical massNumber of molelcules
Total (without water)37,5291
Polymers37,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TYROSINE-PROTEIN KINASE TIE-2


Theoretical massNumber of molelcules
Total (without water)37,5291
Polymers37,5291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.494, 92.887, 70.798
Angle α, β, γ (deg.)90, 108.926, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TYROSINE-PROTEIN KINASE TIE-2


Mass: 37528.812 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: Q02763, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.5% PEG12000, 2.5% glycerol, 100mM Hepes, 10mM spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
220 mMHEPES1drop
3300 mM1dropNaCl
45 mMdithiothreitol1drop
52.5 %PEG120001reservoir
62.5 %glycerol1reservoir
7100 mMHEPES1reservoir
810 mMspermidine1reservoir

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 39864 / Num. obs: 39864 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Num. unique all: 5582 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.2

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4089 -random
Rwork0.225 ---
all0.195 39864 --
obs0.195 39864 96.3 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 0 441 5201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0058

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