[English] 日本語
Yorodumi- PDB-6wfn: Crystal structure of human Naa50 in complex with AcCoA and an inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wfn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4a) identified using DNA encoded library technology | ||||||
Components | N-alpha-acetyltransferase 50 | ||||||
Keywords | TRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / DNA encoded library / AcCoA / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6wfn.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wfn.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 6wfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/6wfn ftp://data.pdbj.org/pub/pdb/validation_reports/wf/6wfn | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19571.502 Da / Num. of mol.: 1 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: Chemical | ChemComp-ACO / |
#3: Chemical | ChemComp-U2J / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.23 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.77 Details: Naa50 apo protein (13.0 mg/ml) was incubated with 4a and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution containing 0.1 M Bis_tris, pH 5.77 and 21% w/v PEG 3350 was mixed ...Details: Naa50 apo protein (13.0 mg/ml) was incubated with 4a and AcCoA in a 1:3:3 molar ratio on ice for 60 min. Reservoir solution containing 0.1 M Bis_tris, pH 5.77 and 21% w/v PEG 3350 was mixed 0.2ul:0.2ul with Naa50:4b:AcCoA complex |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2019 |
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: 1.07→36.11 Å / Num. obs: 55133 / % possible obs: 87.4 % / Redundancy: 3 % / Biso Wilson estimate: 9.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.07→1.13 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2758 / CC1/2: 0.789 / % possible all: 38.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: previously determined in-house structure Resolution: 1.07→36.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.039 / SU Rfree Blow DPI: 0.039 / SU Rfree Cruickshank DPI: 0.038
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.13 Å2 / Biso mean: 16.38 Å2 / Biso min: 5.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.07→36.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.07→1.1 Å / Rfactor Rfree error: 0
|