+Open data
-Basic information
Entry | Database: PDB / ID: 1mqb | ||||||
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Title | Crystal Structure of Ephrin A2 (ephA2) Receptor Protein Kinase | ||||||
Components | Ephrin type-A receptor 2 | ||||||
Keywords | TRANSFERASE / Tyrosine Protein Kinase | ||||||
Function / homology | Function and homology information notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / negative regulation of chemokine production / ephrin receptor activity / leading edge membrane / bone remodeling / post-anal tail morphogenesis / response to growth factor / activation of GTPase activity / regulation of lamellipodium assembly / tight junction / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / vasculogenesis / regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / transmembrane receptor protein tyrosine kinase activity / cell chemotaxis / negative regulation of angiogenesis / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / skeletal system development / molecular function activator activity / cell motility / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / receptor protein-tyrosine kinase / neuron differentiation / ruffle membrane / osteoblast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage / cell migration / virus receptor activity / lamellipodium / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / phosphorylation / focal adhesion / cell surface / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Nowakowski, J. / Cronin, C.N. / McRee, D.E. / Knuth, M.W. / Nelson, C. / Pavletich, N. / Rogers, J. / Sang, B.C. / Scheibe, D.N. / Swanson, R.V. / Thompson, D.A. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structures of the Cancer Related Aurora-A, FAK and EphA2 Protein Kinases from Nanovolume Crystallography Authors: Nowakowski, J. / Cronin, C.N. / McRee, D.E. / Knuth, M.W. / Nelson, C. / Pavletich, N. / Rogers, J. / Sang, B.C. / Scheibe, D.N. / Swanson, R.V. / Thompson, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mqb.cif.gz | 121.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mqb.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/1mqb ftp://data.pdbj.org/pub/pdb/validation_reports/mq/1mqb | HTTPS FTP |
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-Related structure data
Related structure data | 1mp8C 1mq4C 1jpaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37783.410 Da / Num. of mol.: 2 / Fragment: Kinase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EphA2 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29317, EC: 2.7.1.112 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Ethylene Glycol, PEG 10K, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2001 / Details: synchrotron |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 36207 / Num. obs: 35483 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 44.66 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2 / Num. unique all: 1662 / Rsym value: 0.485 / % possible all: 0.78 |
Reflection | *PLUS Lowest resolution: 63 Å / % possible obs: 95 % |
Reflection shell | *PLUS % possible obs: 78 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JPA Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 8.733 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.324 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.668 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 63 Å / Num. reflection obs: 30484 / % reflection Rfree: 5 % / Rfactor Rfree: 0.289 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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