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Yorodumi- PDB-5m8q: Crystal structure of human tyrosinase related protein 1 mutant (T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m8q | |||||||||
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Title | Crystal structure of human tyrosinase related protein 1 mutant (T391V-R374S-Y362F) in complex with kojic acid | |||||||||
Components | 5,6-dihydroxyindole-2-carboxylic acid oxidase | |||||||||
Keywords | UNKNOWN FUNCTION / human tyrosinase related protein 1 / melanin biosynthesis / tyrosinase / oxidoreductase | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / acetoacetic acid metabolic process / Melanin biosynthesis / positive regulation of melanin biosynthetic process / tyrosinase activity / intracellular vesicle / melanocyte differentiation / melanin biosynthetic process / melanosome membrane / melanosome organization ...Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / acetoacetic acid metabolic process / Melanin biosynthesis / positive regulation of melanin biosynthetic process / tyrosinase activity / intracellular vesicle / melanocyte differentiation / melanin biosynthetic process / melanosome membrane / melanosome organization / Regulation of MITF-M-dependent genes involved in pigmentation / clathrin-coated endocytic vesicle membrane / melanosome / oxidoreductase activity / endosome membrane / protein homodimerization activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.85 Å | |||||||||
Authors | Lai, X. / Soler-Lopez, M. / Wichers, H.J. / Dijkstra, B.W. | |||||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Structure of Human Tyrosinase Related Protein 1 Reveals a Binuclear Zinc Active Site Important for Melanogenesis. Authors: Lai, X. / Wichers, H.J. / Soler-Lopez, M. / Dijkstra, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m8q.cif.gz | 363 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m8q.ent.gz | 300.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m8q_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 5m8q_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 5m8q_validation.xml.gz | 70.8 KB | Display | |
Data in CIF | 5m8q_validation.cif.gz | 93.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/5m8q ftp://data.pdbj.org/pub/pdb/validation_reports/m8/5m8q | HTTPS FTP |
-Related structure data
Related structure data | 5m8lC 5m8mC 5m8nC 5m8oC 5m8pC 5m8rC 5m8tC 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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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 50531.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYRP1, CAS2, TYRP, TYRRP / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P17643, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor |
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-Sugars , 6 types, 18 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 17 molecules
#8: Chemical | ChemComp-ZN / #9: Chemical | ChemComp-KOJ / #10: 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: 2.98 Å3/Da / Density % sol: 58.76 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris (pH 7.0), 0.2 M NaCl and 30% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.77 Å / Num. obs: 57320 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 9.9 |
-Processing
Software |
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Refinement | Resolution: 2.85→47.875 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 112 Å2 / Biso mean: 57.1239 Å2 / Biso min: 25.52 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.85→47.875 Å
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