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Yorodumi- PDB-9ey7: Crystal structure of human tyrosinase-related protein 1 (TYRP1) i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9ey7 | ||||||
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Title | Crystal structure of human tyrosinase-related protein 1 (TYRP1) in complex with (R)-2,4-dihydroxyphenylalanine | ||||||
Components | 5,6-dihydroxyindole-2-carboxylic acid oxidase | ||||||
Keywords | METAL BINDING PROTEIN / melanogenesis / human tyrosinase / tyrosinase inhibitor | ||||||
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 / tyrosinase activity / positive regulation of melanin biosynthetic process / melanocyte differentiation / melanin biosynthetic process / melanosome membrane / melanosome organization / intracellular vesicle ...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 / tyrosinase activity / positive regulation of melanin biosynthetic process / melanocyte differentiation / melanin biosynthetic process / melanosome membrane / melanosome organization / intracellular vesicle / 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 / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Ng, Y.M. / Soler-Lopez, M. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Chembiochem / Year: 2024 Title: Interactions of Phenylalanine Derivatives with Human Tyrosinase: Lessons from Experimental and Theoretical tudies. Authors: Faure, C. / Min Ng, Y. / Belle, C. / Soler-Lopez, M. / Khettabi, L. / Saidi, M. / Berthet, N. / Maresca, M. / Philouze, C. / Rachidi, W. / Reglier, M. / du Moulinet d'Hardemare, A. / Jamet, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9ey7.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9ey7.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 9ey7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9ey7_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 9ey7_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 9ey7_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 9ey7_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/9ey7 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/9ey7 | HTTPS FTP |
-Related structure data
Related structure data | 9ey5C 9ey6C 9ey8C 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, 1 molecules A
#1: Protein | Mass: 50776.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TYRP1, CAS2, TYRP, TYRRP / Plasmid: pACEBac1 / Cell (production host): Insect cell / Cell line (production host): Sf21 / 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 , 4 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-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 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 | ||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
-Non-polymers , 4 types, 66 molecules
#6: Chemical | #7: Chemical | ChemComp-ZN / #8: Chemical | ChemComp-OTY / | #9: Water | ChemComp-HOH / | |
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-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: 4.19 Å3/Da / Density % sol: 70.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, Zinc chloride, Tris-HCl pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8856, 1.2782, 1.7220 | ||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 11, 2022 | ||||||||||||
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.607→48.33 Å / Num. obs: 47641 / % possible obs: 98.63 % / Redundancy: 3.3 % / Biso Wilson estimate: 56.46 Å2 / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.1412 / Rpim(I) all: 0.08136 / Rrim(I) all: 0.164 / Net I/σ(I): 4.94 | ||||||||||||
Reflection shell | Resolution: 2.61→2.7 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6955 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 4767 / CC1/2: 0.598 / CC star: 0.865 / Rpim(I) all: 0.4014 / Rrim(I) all: 0.8078 / % possible all: 98.33 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→48.33 Å / SU ML: 0.3284 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7296 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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