+Open data
-Basic information
Entry | Database: PDB / ID: 6wh8 | |||||||||
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Title | The structure of NTMT1 in complex with compound BM-30 | |||||||||
Components |
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Keywords | TRANSFERASE / methyltransferase / enzyme / inhibitor complex / transferase-transferase inhibitor complex | |||||||||
Function / homology | Function and homology information N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal peptidyl-proline dimethylation / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 Å | |||||||||
Authors | Noinaj, N. / Chen, D. / Huang, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Selective Peptidomimetic Inhibitors of NTMT1/2: Rational Design, Synthesis, Characterization, and Crystallographic Studies. Authors: Mackie, B.D. / Chen, D. / Dong, G. / Dong, C. / Parker, H. / Schaner Tooley, C.E. / Noinaj, N. / Min, J. / Huang, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wh8.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wh8.ent.gz | 157.9 KB | Display | PDB format |
PDBx/mmJSON format | 6wh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/6wh8 ftp://data.pdbj.org/pub/pdb/validation_reports/wh/6wh8 | HTTPS FTP |
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-Related structure data
Related structure data | 5e1dS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27320.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9BV86, protein N-terminal methyltransferase #2: Protein/peptide | #3: Chemical | #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: 3.04 Å3/Da / Density % sol: 59.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na-HEPES, pH 7.5, 1.6 M ammonium sulfate, and 2% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.729→29.55 Å / Num. obs: 72963 / % possible obs: 99.9 % / Redundancy: 19.4 % / Rpim(I) all: 0.069 / Rrim(I) all: 0.224 / Rsym value: 0.213 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.729→1.76 Å / Redundancy: 18.7 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3997 / Rpim(I) all: 1.516 / Rrim(I) all: 4.823 / Rsym value: 4.575 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5E1D Resolution: 1.729→29.55 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.729→29.55 Å
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Refine LS restraints |
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LS refinement shell |
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