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Yorodumi- PDB-7twu: Crystal structure of human phenylethanolamine N-methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7twu | ||||||
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Title | Crystal structure of human phenylethanolamine N-methyltransferase (PNMT) in complex with (2S)-2-amino-4-(((5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl)(4-(7,8-dichloro-1,2,3,4-tetrahydroisoquinolin-4-yl)butyl)amino)butanoic acid and AdoHcy (SAH) | ||||||
Components | Phenylethanolamine N-methyltransferase | ||||||
Keywords | TRANSFERASE / Transition state analogue / Chemical synthesis / Drug design / 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: 2.1 Å | ||||||
Authors | Harijan, R.K. / Mahmoodi, N. / Minnow, Y.V.T. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Cell-Effective Transition-State Analogue of Phenylethanolamine N -Methyltransferase. Authors: Mahmoodi, N. / Minnow, Y.V.T. / Harijan, R.K. / Bedard, G.T. / 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 | 7twu.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7twu.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 7twu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7twu_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7twu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7twu_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 7twu_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tw/7twu ftp://data.pdbj.org/pub/pdb/validation_reports/tw/7twu | HTTPS FTP |
-Related structure data
Related structure data | 7tx2C 4mikS 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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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 , 5 types, 138 molecules
#2: Chemical | ChemComp-SAH / | ||||
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#3: Chemical | ChemComp-CD / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-KNX / | #6: 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: 3.2 Å3/Da / Density % sol: 61.54 % |
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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, 18 % 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: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Sep 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→93.75 Å / Num. obs: 49863 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3995 / CC1/2: 0.83 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MIK Resolution: 2.1→38.369 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.11 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.75 Å2 / Biso mean: 61.4207 Å2 / Biso min: 38.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→38.369 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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