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Yorodumi- PDB-6i99: Bone Marrow Tyrosine Kinase in Chromosome X in complex with a new... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i99 | ||||||||||||
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Title | Bone Marrow Tyrosine Kinase in Chromosome X in complex with a newly designed covalent inhibitor JS24 | ||||||||||||
Components | Cytoplasmic tyrosine-protein kinase BMX | ||||||||||||
Keywords | CYTOSOLIC PROTEIN / Cytoplasmic tyrosine-kinase BMX / Homo Sapiens | ||||||||||||
Function / homology | Function and homology information phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / adaptive immune response ...phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / adaptive immune response / protein autophosphorylation / cell adhesion / intracellular signal transduction / protein phosphorylation / apoptotic process / signal transduction / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||||||||
Authors | Sousa, B.B. / Matias, P.M. / Marques, M.C. / Seixas, J.D. / Bernardes, G.J.L. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Chem.Biol. / Year: 2020 Title: Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors Authors: Seixas, J.D. / Sousa, B.B. / Marques, M.C. / Guerreiro, A. / Traquete, R. / Rodrigues, T. / Albuquerque, I.S. / Sousa, M.F.Q. / Lemos, A.R. / Sousa, P.M.F. / Bandeiras, T.M. / Wu, D. / ...Authors: Seixas, J.D. / Sousa, B.B. / Marques, M.C. / Guerreiro, A. / Traquete, R. / Rodrigues, T. / Albuquerque, I.S. / Sousa, M.F.Q. / Lemos, A.R. / Sousa, P.M.F. / Bandeiras, T.M. / Wu, D. / Doyle, S.K. / Robinson, C.V. / Koehler, A.N. / Corzana, F. / Matias, P.M. / Bernardes, G.J.L. #1: Journal: Chemrxiv / Year: 2020 Title: Rationally Designed Potent BMX Inhibitors Reveals Mode of Covalent Binding at the Atomic Level Authors: Seixas, J.D. / Sousa, B.B. / Marques, M.C. / Guerreiro, A. / Traquete, R. / Rodrigues, T. / Albuquerque, I.S. / Sousa, M.F.Q. / Lemos, A.R. / Sousa, P.M.F. / Bandeiras, T.M. / Wu, D. / ...Authors: Seixas, J.D. / Sousa, B.B. / Marques, M.C. / Guerreiro, A. / Traquete, R. / Rodrigues, T. / Albuquerque, I.S. / Sousa, M.F.Q. / Lemos, A.R. / Sousa, P.M.F. / Bandeiras, T.M. / Wu, D. / Doyle, S.K. / Robinson, C.V. / Koehler, A.N. / Corzana, F. / Matias, P.M. / Bernardes, G.J.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i99.cif.gz | 319.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i99.ent.gz | 265.8 KB | Display | PDB format |
PDBx/mmJSON format | 6i99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/6i99 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/6i99 | HTTPS FTP |
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-Related structure data
Related structure data | 3sxsS 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: 32564.414 Da / Num. of mol.: 2 / Mutation: Q432K, Q620E, Q611M, D617T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: Hematopoietic, endothelial, metastatic carcinoma / Gene: BMX / Variant: 2 / Plasmid: pFastBac1 / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: P51813, non-specific protein-tyrosine kinase #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: 2.35 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: imidazole-malate, PEG 600 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→72.6 Å / Num. obs: 23531 / % possible obs: 87.6 % / Redundancy: 4.2 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.101 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.98→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1161 / CC1/2: 0.586 / Rpim(I) all: 0.489 / % possible all: 51.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SXS Resolution: 2.001→72.559 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 31.26 Details: NCS used between chain A and chain B TLS refinement of anisotropic ADPs - 4 non-equivalent rigid bodies were defined per protein chain. Hydrogen atoms were included in calculated positions.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: -2.2119 Å2 / ksol: 0.9549 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→72.559 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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