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- PDB-3zew: Crystal structure of EphB4 in complex with staurosporine -

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Basic information

Entry
Database: PDB / ID: 3zew
TitleCrystal structure of EphB4 in complex with staurosporine
ComponentsEPHRIN TYPE-B RECEPTOR 4
KeywordsTRANSFERASE / INHIBITOR
Function / homology
Function and homology information


ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol
Similarity search - Function
Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain ...Ephrin type-B receptor 4, ligand binding domain / EPH-B4, SAM domain / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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
STAUROSPORINE / Ephrin type-B receptor 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDebreczeni, J.E. / Overman, R. / Truman, C. / McAlister, M. / Attwood, T.K.
CitationJournal: Protein Sci. / Year: 2014
Title: Completing the Structural Family Portrait of the Human Ephb Tyrosine Kinase Domains
Authors: Overman, R.C. / Debreczeni, J.E. / Truman, C.M. / Mcalister, M.S. / Attwood, T.K.
History
DepositionDec 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3May 7, 2014Group: Database references
Revision 1.4Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPHRIN TYPE-B RECEPTOR 4
B: EPHRIN TYPE-B RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5248
Polymers67,2072
Non-polymers1,3176
Water1,982110
1
A: EPHRIN TYPE-B RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2624
Polymers33,6031
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPHRIN TYPE-B RECEPTOR 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2624
Polymers33,6031
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.170, 88.710, 80.780
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EPHRIN TYPE-B RECEPTOR 4 / EPHB4 / HEPATOMA TRANSMEMBRANE KINASE / TYROSINE-PROTEIN KINASE TYRO11


Mass: 33603.273 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 598-892
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P54760, receptor protein-tyrosine kinase
#2: Chemical ChemComp-STU / STAUROSPORINE / Staurosporine


Mass: 466.531 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: anticancer, antifungal, antibiotic, alkaloid*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.09 Å3/Da / Density % sol: 60.26 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU SATURN / Detector: CCD / Date: Jul 19, 2009 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→33.42 Å / Num. obs: 22752 / % possible obs: 91.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.22 % / Biso Wilson estimate: 65.75 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.4 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
d*TREKdata reduction
DTSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.9227 / Cor.coef. Fo:Fc free: 0.875 / SU R Cruickshank DPI: 0.532 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.506 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.313
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 1156 5.11 %RANDOM
Rwork0.2379 ---
obs0.2401 22618 91.21 %-
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.8738 Å20 Å20.045 Å2
2---1.1673 Å20 Å2
3---0.2935 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 90 110 4233
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094236HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035774HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1438SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes687HARMONIC5
X-RAY DIFFRACTIONt_it4236HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion17.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion556SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4961SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2812 150 5.07 %
Rwork0.245 2806 -
all0.2467 2956 -
obs--91.21 %

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