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Yorodumi- PDB-2g72: Structure of hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g72 | ||||||
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Title | Structure of hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholinosulfonamide-THIQ and AdoMet | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
Function / homology | Function and homology information phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Tyndall, J.D.A. / Gee, C.L. / Martin, J.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase Authors: Gee, C.L. / Drinkwater, N. / Tyndall, J.D.A. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g72.cif.gz | 126.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g72.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 2g72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g72_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2g72_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2g72_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2g72_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/2g72 ftp://data.pdbj.org/pub/pdb/validation_reports/g7/2g72 | HTTPS FTP |
-Related structure data
Related structure data | 2g70C 2g71C 2obfC 2onyC 2onzC 2opbC 1hnnS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 31845.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: pnmt / Plasmid: PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P11086, phenylethanolamine N-methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.3 Å3/Da / Density % sol: 62.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: PEG6K, LiCl, cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2004 |
Radiation | Monochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→32.84 Å / Num. obs: 58197 / % possible obs: 99.8 % / Redundancy: 11.71 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.99 / Net I/σ(I): 17.5 / Scaling rejects: 5149 |
Reflection shell | Resolution: 2→2.07 Å / % possible obs: 99 % / Redundancy: 11.38 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.6 / Num. measured all: 64721 / Num. unique all: 5662 / Num. unique obs: 5662 / Χ2: 1.16 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1HNN Resolution: 2→31.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3067226.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.823 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→31.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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