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Open data
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Basic information
Entry | Database: PDB / ID: 8trt | |||||||||
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Title | Structure of the EphA2 CRD bound to FabS1CE_C1, monoclinic form | |||||||||
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Function / homology | ![]() 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 / leading edge membrane / negative regulation of chemokine production / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Singer, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / Atwell, S. / Kossiakoff, A.A. / Sidhu, S.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 444.5 KB | Display | ![]() |
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PDB format | ![]() | 346.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8t58C ![]() 8t6iC ![]() 8t7fC ![]() 8t7gC ![]() 8t7iC ![]() 8t8iC ![]() 8t9yC ![]() 8trsSC ![]() 8ts5C ![]() 8trv S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules ED
#3: Protein | Mass: 13961.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): expressed with a C-terminal thrombin cleavage site and 6-his sequence. The residues LTPR at the C-terminus are derived from the thrombin cleavage site Cell line (production host): Expi293 / Production host: ![]() ![]() References: UniProt: P29317, ![]() |
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-Antibody , 2 types, 4 molecules ABGC
#1: Antibody | Mass: 23883.762 Da / Num. of mol.: 2 / Mutation: SSASTK replaced by FNQIK Source method: isolated from a genetically manipulated source Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23432.895 Da / Num. of mol.: 2 / Mutation: SPHAGLSSP replaced by QGTTS; Q165S, K167Y Source method: isolated from a genetically manipulated source Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/CL.gif)
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![](data/chem/img/HOH.gif)
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#4: Chemical | ChemComp-CL / ![]() #5: Chemical | #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.39 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 200 mM sodium chloride, 100 mM Bis-Tris, 20% PEG3350 Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2022 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→68.78 Å / Num. obs: 32852 / % possible obs: 97 % / Redundancy: 6.6 % / Biso Wilson estimate: 58.06 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.079 / Rrim(I) all: 0.211 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.9→3.04 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4372 / CC1/2: 0.783 / Rpim(I) all: 0.384 / Rrim(I) all: 0.959 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 8TRS Resolution: 3→68.78 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.7589 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→68.78 Å
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Refine LS restraints |
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LS refinement shell |
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