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- PDB-3kpy: Crystal Structure of hPNMT in Complex AdoHcy and 6-Chlorooxindole -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kpy | ||||||
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Title | Crystal Structure of hPNMT in Complex AdoHcy and 6-Chlorooxindole | ||||||
![]() | Phenylethanolamine N-methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / fragment screening / Catecholamine biosynthesis / S-adenosyl-L-methionine | ||||||
Function / homology | ![]() phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Drinkwater, N. / Martin, J.L. | ||||||
![]() | ![]() Title: Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors. Authors: Drinkwater, N. / Vu, H. / Lovell, K.M. / Criscione, K.R. / Collins, B.M. / Prisinzano, T.E. / Poulsen, S.A. / McLeish, M.J. / Grunewald, G.L. / Martin, J.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 231.1 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 939.6 KB | Display | ![]() |
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Full document | ![]() | 950.3 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kpjC ![]() 3kpuC ![]() 3kpvC ![]() 3kpwC ![]() 3kqmC ![]() 3kqoC ![]() 3kqpC ![]() 3kqqC ![]() 3kqsC ![]() 3kqtC ![]() 3kqvC ![]() 3kqwC ![]() 3kqyC ![]() 3kr0C ![]() 3kr1C ![]() 3kr2C ![]() 1hnnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P11086, phenylethanolamine N-methyltransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 6, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: OSMIC VARI-MAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→45.56 Å / Num. obs: 30511 / % possible obs: 90.2 % / Redundancy: 4.91 % / Rmerge(I) obs: 0.096 / Χ2: 0.96 / Net I/σ(I): 8.6 / Scaling rejects: 1134 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Starting model: PDB entry 1HNN Resolution: 2.4→45.563 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.785 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.791 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.55 Å2 / Biso mean: 42.447 Å2 / Biso min: 18.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→45.563 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 24.0715 Å / Origin y: 51.1323 Å / Origin z: -5.8487 Å
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Refinement TLS group |
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