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Yorodumi- PDB-6wf3: Crystal structure of human Naa50 in complex with a cofactor deriv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wf3 | ||||||
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Title | Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) | ||||||
Components |
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Keywords | TRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...peptidyl-lysine acetyltransferase activity / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å | ||||||
Authors | Greasley, S.E. / Feng, J. / Deng, Y.-L. / Stewart, A.E. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Characterization of SpecificN-alpha-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / ...Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / Meier, J. / Meng, X. / Montano, J.L. / Morgan, B.A. / Naughton, B.S. / Palde, P.B. / Paul, T.A. / Richardson, P. / Sakata, S. / Shaginian, A. / Sonnenburg, W.K. / Subramanyam, C. / Timofeevski, S. / Wan, J. / Yan, W. / Stewart, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wf3.cif.gz | 221.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wf3.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/6wf3 ftp://data.pdbj.org/pub/pdb/validation_reports/wf/6wf3 | HTTPS FTP |
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-Related structure data
Related structure data | 6wf5C 6wfgC 6wfkC 6wfnC 6wfoC 2ob0S S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 19571.502 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9GZZ1, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Protein/peptide | Mass: 440.581 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-COA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 286.15 K / Method: vapor diffusion, sitting drop Details: Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1: ...Details: Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→53.71 Å / Num. obs: 56682 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.29→2.41 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Num. unique obs: 8301 / CC1/2: 0.785 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Ob0 Resolution: 2.291→53.71 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.273 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.211
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Displacement parameters | Biso mean: 56.03 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.291→53.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.291→2.31 Å
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