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Yorodumi- PDB-7rkk: Structure of Nicotinamide N-Methyltransferase (NNMT) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rkk | ||||||
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Title | Structure of Nicotinamide N-Methyltransferase (NNMT) in complex with II399 (C2 space group) | ||||||
Components | NNMT protein | ||||||
Keywords | TRANSFERASE/INHIBITOR / Methyltransferase / Inhibitor / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information nicotinamide metabolic process / nicotinamide N-methyltransferase activity / positive regulation of protein deacetylation / : / animal organ regeneration / positive regulation of gluconeogenesis / methylation / response to xenobiotic stimulus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Yadav, R. / Noinaj, N. / Iyamu, I.D. / Huang, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2022 Title: Exploring Unconventional SAM Analogues To Build Cell-Potent Bisubstrate Inhibitors for Nicotinamide N-Methyltransferase. Authors: Iyamu, I.D. / Vilseck, J.Z. / Yadav, R. / Noinaj, N. / Huang, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rkk.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rkk.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 7rkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rkk_validation.pdf.gz | 965.6 KB | Display | wwPDB validaton report |
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Full document | 7rkk_full_validation.pdf.gz | 973.3 KB | Display | |
Data in XML | 7rkk_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7rkk_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rkk ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rkk | HTTPS FTP |
-Related structure data
Related structure data | 7rklC 6pveS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.0737065701142, 0.0731618716335, 0.994592721701), (0.0460713766967, -0.995990847394, 0.0766789420614), (0.996215222616, 0.0514739977607, 0.0700404010787)Vector: -16. ...NCS oper: (Code: given Matrix: (-0.0737065701142, 0.0731618716335, 0.994592721701), Vector: |
-Components
#1: Protein | Mass: 31466.033 Da / Num. of mol.: 2 / Mutation: K100A, E101A, E103A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT, hCG_39357 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FH49 #2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 36.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→50 Å / Num. obs: 11173 / % possible obs: 90.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 36.34 Å2 / CC1/2: 0.938 / CC star: 0.984 / Rpim(I) all: 0.151 / Rrim(I) all: 0.369 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 5.5 % / Num. unique obs: 1112 / CC1/2: 0.351 / CC star: 0.721 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6PVE Resolution: 2.76→46.01 Å / SU ML: 0.4389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9719 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→46.01 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.99171088819 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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