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Yorodumi- PDB-6wx5: Adducts formed after 3 weeks in the reaction of chlorido[chlorido... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wx5 | ||||||
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Title | Adducts formed after 3 weeks in the reaction of chlorido[chlorido(2,2'-((2-([2,2':6',2''-Terpyridin]-4'-yloxy)ethyl)azanediyl)bis(ethan-1-ol))platinum(II)] with HEWL | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / metal-based / anticancer / platinum / Terpyridine / lysozyme / metallodrug | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Sullivan, M.P. / Hartinger, C.G. / Goldstone, D.C. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2021 Title: Mustards-Derived Terpyridine-Platinum Complexes as Anticancer Agents: DNA Alkylation vs Coordination. Authors: Adams, M. / Sullivan, M.P. / Tong, K.K.H. / Goldstone, D.C. / Hanif, M. / Jamieson, S.M.F. / Hartinger, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wx5.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wx5.ent.gz | 50.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wx/6wx5 ftp://data.pdbj.org/pub/pdb/validation_reports/wx/6wx5 | HTTPS FTP |
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-Related structure data
Related structure data | 4nhiS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, UniProt: P00698*PLUS, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-PT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.1 M Sodium Acetate pH 4.7 and 0.8 M Sodium Chloride pH 4.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 25, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→38.61 Å / Num. obs: 29331 / % possible obs: 99.7 % / Redundancy: 18.3 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.015 / Rrim(I) all: 0.064 / Net I/σ(I): 37.3 / Num. measured all: 537924 / Scaling rejects: 417 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NHI Resolution: 1.3→34.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.031 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0581 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 200.57 Å2 / Biso mean: 16.824 Å2 / Biso min: 10.04 Å2
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Refinement step | Cycle: final / Resolution: 1.3→34.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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