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Yorodumi- PDB-4mpx: Human beta-tryptase co-crystal structure with [(1,1,3,3-tetrameth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mpx | ||||||
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Title | Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) | ||||||
Components | Tryptase alpha/beta-1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / coferon / alpha-hydroxyketone / small molecule inhibitor / drug discovery / self-assembly / crystal catalysis / silanol / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information tryptase / Activation of Matrix Metalloproteinases / extracellular matrix disassembly / serine-type peptidase activity / defense response / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | White, A. / Stein, A.J. / Suto, R. | ||||||
Citation | Journal: To be Published Title: Target-directed self-assembly of homodimeric drugs Authors: Giardina, S.F. / Pingle, M. / Foreman, K.W. / Werner, D.S. / Bergstrom, D.E. / Barany, F. / Arnold, L.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mpx.cif.gz | 113.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mpx.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mpx_validation.pdf.gz | 716.5 KB | Display | wwPDB validaton report |
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Full document | 4mpx_full_validation.pdf.gz | 721.9 KB | Display | |
Data in XML | 4mpx_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 4mpx_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/4mpx ftp://data.pdbj.org/pub/pdb/validation_reports/mp/4mpx | HTTPS FTP |
-Related 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27491.426 Da / Num. of mol.: 2 / Fragment: UNP residues 31-275 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPS1, TPS2, TPSAB1, TPSB1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q15661, tryptase |
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-Non-polymers , 6 types, 320 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-2AV / [( | #6: Chemical | ChemComp-MES / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | N132K IS A NATURAL VARIANT. |
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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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.9 mg/mL protein incubated with compound 6A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. all: 40628 / Num. obs: 40587 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Χ2: 1.29 / Net I/σ(I): 8.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.832 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber
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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: 92.18 Å2 / Biso mean: 31.6509 Å2 / Biso min: 16.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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