[English] 日本語
Yorodumi- PDB-7kpu: Crystal structure of human NatD (NAA40) bound to a bisubstrate an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kpu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue with a C-3 linker | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / acetyl transferase / NAA40 / NatD / bisubstrate | ||||||
Function / homology | Function and homology information N-terminal L-serine Nalpha-acetyltransferase NatD / histone H2A acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / centriolar satellite / lipid metabolic process / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | ||||||
Authors | Deng, S. / Marmorstein, R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D. Authors: Deng, Y. / Deng, S. / Ho, Y.H. / Gardner, S.M. / Huang, Z. / Marmorstein, R. / Huang, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7kpu.cif.gz | 215.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7kpu.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 7kpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/7kpu ftp://data.pdbj.org/pub/pdb/validation_reports/kp/7kpu | HTTPS FTP |
---|
-Related structure data
Related structure data | 7kd7C 4u9wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
-Protein / Protein/peptide , 2 types, 4 molecules DAEB
#1: Protein | Mass: 23697.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NAA40, NAT11, PATT1 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: Q86UY6, N-terminal L-serine Nalpha-acetyltransferase NatD #2: Protein/peptide | Mass: 505.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|
-Non-polymers , 7 types, 437 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BTB / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-tris, pH 5.5, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→127.02 Å / Num. obs: 81356 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.43→1.45 Å / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 3986 / CC1/2: 0.961 / Rpim(I) all: 0.12 / Rrim(I) all: 0.295 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4U9W Resolution: 1.43→64.05 Å / SU ML: 0.117 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 17.3216 / Stereochemistry target values: CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→64.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|