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Yorodumi- PDB-6gq3: Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gq3 | ||||||
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Title | Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-L-norleucine (DON) at 1.85 A resolution | ||||||
Components | Asparagine synthetase [glutamine-hydrolyzing] | ||||||
Keywords | BIOSYNTHETIC PROTEIN / L-asparagine biosynthesis / breast cancer / inhibitor development | ||||||
Function / homology | Function and homology information asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / aspartate family amino acid metabolic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / response to follicle-stimulating hormone / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / response to methotrexate ...asparagine synthase (glutamine-hydrolysing) / L-asparagine biosynthetic process / aspartate family amino acid metabolic process / asparagine synthase (glutamine-hydrolyzing) activity / asparagine biosynthetic process / response to follicle-stimulating hormone / Response of EIF2AK1 (HRI) to heme deficiency / Aspartate and asparagine metabolism / ATF4 activates genes in response to endoplasmic reticulum stress / response to methotrexate / glutamine metabolic process / Response of EIF2AK4 (GCN2) to amino acid deficiency / response to light stimulus / cellular response to glucose starvation / response to amino acid / response to mechanical stimulus / cellular response to hormone stimulus / positive regulation of mitotic cell cycle / liver development / response to toxic substance / negative regulation of apoptotic process / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Zhu, W. / Radadiya, A. / Bisson, C. / Jin, Y. / Nordin, B.E. / Imasaki, T. / Wenzel, S. / Sedelnikova, S.E. / Berry, A.H. / Nomanbhoy, T.K. ...Zhu, W. / Radadiya, A. / Bisson, C. / Jin, Y. / Nordin, B.E. / Imasaki, T. / Wenzel, S. / Sedelnikova, S.E. / Berry, A.H. / Nomanbhoy, T.K. / Kozarich, J.W. / Takagi, Y. / Rice, D.W. / Richards, N.G.J. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: High-resolution crystal structure of human asparagine synthetase enables analysis of inhibitor binding and selectivity. Authors: Zhu, W. / Radadiya, A. / Bisson, C. / Wenzel, S. / Nordin, B.E. / Martinez-Marquez, F. / Imasaki, T. / Sedelnikova, S.E. / Coricello, A. / Baumann, P. / Berry, A.H. / Nomanbhoy, T.K. / ...Authors: Zhu, W. / Radadiya, A. / Bisson, C. / Wenzel, S. / Nordin, B.E. / Martinez-Marquez, F. / Imasaki, T. / Sedelnikova, S.E. / Coricello, A. / Baumann, P. / Berry, A.H. / Nomanbhoy, T.K. / Kozarich, J.W. / Jin, Y. / Rice, D.W. / Takagi, Y. / Richards, N.G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gq3.cif.gz | 232.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gq3.ent.gz | 183.5 KB | Display | PDB format |
PDBx/mmJSON format | 6gq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/6gq3 ftp://data.pdbj.org/pub/pdb/validation_reports/gq/6gq3 | HTTPS FTP |
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-Related structure data
Related structure data | 1ct9S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64455.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Missing loops: 210-223 and 466-480. No electron density for C-terminus: 535-561 Source: (gene. exp.) Homo sapiens (human) / Gene: ASNS, TS11 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P08243, asparagine synthase (glutamine-hydrolysing) |
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-Non-polymers , 5 types, 578 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: 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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M NaCl, 0.1 M sodium HEPES buffer, pH 7.5, and 12% w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→33.65 Å / Num. obs: 100002 / % possible obs: 99.8 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.067 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.794 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4932 / CC1/2: 0.512 / Rpim(I) all: 0.624 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CT9 Resolution: 1.85→33.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.395 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.129 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.556 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→33.65 Å
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