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Yorodumi- PDB-6i6x: New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i6x | |||||||||
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Title | New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes | |||||||||
Components | (Alpha-L-iduronidase) x 2 | |||||||||
Keywords | HYDROLASE / Iduronidase Inhibitors GH39 | |||||||||
Function / homology | Function and homology information L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation ...L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal lumen / signaling receptor binding / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å | |||||||||
Authors | Gloster, T.M. / McMahon, S.A. / Oehler, V. | |||||||||
Citation | Journal: Chemistry / Year: 2018 Title: New Irreversible alpha-l-Iduronidase Inhibitors and Activity-Based Probes. Authors: Artola, M. / Kuo, C.L. / McMahon, S.A. / Oehler, V. / Hansen, T. / van der Lienden, M. / He, X. / van den Elst, H. / Florea, B.I. / Kermode, A.R. / van der Marel, G.A. / Gloster, T.M. / ...Authors: Artola, M. / Kuo, C.L. / McMahon, S.A. / Oehler, V. / Hansen, T. / van der Lienden, M. / He, X. / van den Elst, H. / Florea, B.I. / Kermode, A.R. / van der Marel, G.A. / Gloster, T.M. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i6x.cif.gz | 266.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i6x.ent.gz | 208.5 KB | Display | PDB format |
PDBx/mmJSON format | 6i6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i6x_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6i6x_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6i6x_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 6i6x_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/6i6x ftp://data.pdbj.org/pub/pdb/validation_reports/i6/6i6x | HTTPS FTP |
-Related structure data
Related structure data | 6i6rC 3w81S C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 27 - 642 / Label seq-ID: 1 - 616
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 70082.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35475, L-iduronidase |
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#2: Protein | Mass: 70053.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35475, L-iduronidase |
-Sugars , 4 types, 6 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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 #6: Sugar | |
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-Non-polymers , 5 types, 309 molecules
#7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Chemical | #11: 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: 2.11 Å3/Da / Density % sol: 41.6 % / Description: rhomboid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.26 M Sodium potassium tartrate, 20 % w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.39→29.73 Å / Num. obs: 69796 / % possible obs: 99.6 % / Redundancy: 5.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.061 / Rrim(I) all: 0.138 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.39→2.44 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 15903 / CC1/2: 0.699 / Rpim(I) all: 0.433 / Rrim(I) all: 0.97 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3w81 Resolution: 2.39→29.73 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.636 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.206 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.978 Å2
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Refinement step | Cycle: 1 / Resolution: 2.39→29.73 Å
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Refine LS restraints |
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