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Yorodumi- PDB-6ws1: Crystal structure of human phenylethanolamine N-methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ws1 | ||||||
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Title | Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-((((2R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(3-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)propyl)amino)butanoic acid and AdoHcy (SAH) | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Transition state analogue / Chemical synthesis / Drug design / Structural Biology / neurodegenerative disease / PNMT | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Harijan, R.K. / Mahmoodi, N. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Transition-State Analogues of PhenylethanolamineN-Methyltransferase. Authors: Mahmoodi, N. / Harijan, R.K. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ws1.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ws1.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ws1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ws1_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6ws1_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6ws1_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 6ws1_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/6ws1 ftp://data.pdbj.org/pub/pdb/validation_reports/ws/6ws1 | HTTPS FTP |
-Related structure data
Related structure data | 4mikS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32327.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PNMT, PENT / Production host: Escherichia coli (E. coli) References: UniProt: P11086, phenylethanolamine N-methyltransferase |
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-Non-polymers , 6 types, 18 molecules
#2: Chemical | ChemComp-SAH / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-CD / | #5: Chemical | ChemComp-K / | #6: Chemical | ChemComp-U87 / | #7: Water | ChemComp-HOH / | |
-Details
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: 3.3 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM Sodium Cacodylate pH 5.5, 170 mM LiCl, 12 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2019 / Details: KB mirrors |
Radiation | Monochromator: Kohzu HLD-15 Double Crystal cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→94.14 Å / Num. obs: 22471 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.76→2.91 Å / Redundancy: 14.7 % / Rmerge(I) obs: 3.3 / Mean I/σ(I) obs: 1 / Num. unique obs: 3196 / CC1/2: 0.69 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MIK Resolution: 2.76→66.476 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.39 Å2 / Biso mean: 88.4198 Å2 / Biso min: 55.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.76→66.476 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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