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Yorodumi- PDB-2aou: Histamine Methyltransferase Complexed with the Antimalarial Drug ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aou | ||||||
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Title | Histamine Methyltransferase Complexed with the Antimalarial Drug Amodiaquine | ||||||
Components | (Histamine N-methyltransferase) x 2 | ||||||
Keywords | TRANSFERASE / CLASSIC METHYLTRANSFERASE FOLD / PROTEIN-DRUG COMPLEX | ||||||
Function / homology | Function and homology information histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Horton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural basis for inhibition of histamine N-methyltransferase by diverse drugs Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X. #1: Journal: Structure / Year: 2001 Title: Polymorphic Forms of Human Histamine Methyltransferase: Structural, Thermal, and Kinetic Comparisons Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X. | ||||||
History |
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Remark 600 | HETEROGEN Any one of the three ethyl groups on ligand, CQA 400 could be the alternative ...HETEROGEN Any one of the three ethyl groups on ligand, CQA 400 could be the alternative conformation of the other two (by the rotation of approximately 120 or 240 drgrees). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aou.cif.gz | 135.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aou.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 2aou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aou_validation.pdf.gz | 701.9 KB | Display | wwPDB validaton report |
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Full document | 2aou_full_validation.pdf.gz | 722.7 KB | Display | |
Data in XML | 2aou_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 2aou_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/2aou ftp://data.pdbj.org/pub/pdb/validation_reports/ao/2aou | HTTPS FTP |
-Related structure data
Related structure data | 2aotC 2aovC 2aowC 2aoxC 1jqdS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33349.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P50135, histamine N-methyltransferase | ||
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#2: Protein | Mass: 33349.020 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P50135 | ||
#3: Chemical | ChemComp-CQA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, MES, ethyleneglycol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2000 |
Radiation | Monochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 27645 / Num. obs: 26928 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.3→2.35 Å / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1JQD Resolution: 2.3→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.35 Å / Rfactor Rfree error: 0.024 /
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