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Yorodumi- PDB-3q2h: Adamts1 in complex with N-hydroxyformamide inhibitors of ADAM-TS4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q2h | ||||||
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Title | Adamts1 in complex with N-hydroxyformamide inhibitors of ADAM-TS4 | ||||||
Components | A disintegrin and metalloproteinase with thrombospondin motifs 1 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Adamts1 Zn-Metalloprotease / disintegrin / metalloproteinase / thrombospondin motifs / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / positive regulation of G1/S transition of mitotic cell cycle / basement membrane / negative regulation of angiogenesis / positive regulation of vascular associated smooth muscle cell proliferation ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / positive regulation of G1/S transition of mitotic cell cycle / basement membrane / negative regulation of angiogenesis / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix / extracellular matrix organization / kidney development / integrin-mediated signaling pathway / metalloendopeptidase activity / metallopeptidase activity / heparin binding / cytoplasmic vesicle / negative regulation of cell population proliferation / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Gerhardt, S. / Hargreaves, D. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: The design and synthesis of novel N-hydroxyformamide inhibitors of ADAM-TS4 for the treatment of osteoarthritis Authors: De Savi, C. / Pape, A. / Cumming, J.G. / Ting, A. / Smith, P.D. / Burrows, J.N. / Mills, M. / Davies, C. / Lamont, S. / Milne, D. / Cook, C. / Moore, P. / Sawyer, Y. / Gerhardt, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q2h.cif.gz | 241.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q2h.ent.gz | 195.4 KB | Display | PDB format |
PDBx/mmJSON format | 3q2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q2h_validation.pdf.gz | 982.5 KB | Display | wwPDB validaton report |
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Full document | 3q2h_full_validation.pdf.gz | 1006.9 KB | Display | |
Data in XML | 3q2h_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 3q2h_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/3q2h ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q2h | HTTPS FTP |
-Related structure data
Related structure data | 3q2gC 2jihS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32578.551 Da / Num. of mol.: 2 / Fragment: residues in UNP 256-548 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q9UHI8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 7 types, 127 molecules
#2: Chemical | #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-NI / #5: Chemical | #6: Chemical | ChemComp-NA / #7: Chemical | #8: 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: 2.74 Å3/Da / Density % sol: 55.09 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å |
Detector | Date: Jan 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.01 Å / Num. obs: 29956 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 4.75 % / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JIH Resolution: 2.33→27.7 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.526 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.44 Å2 / Biso mean: 84.85 Å2 / Biso min: 40.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→27.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.39 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 23.1783 Å / Origin y: -0.182 Å / Origin z: 28.3634 Å
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Refinement TLS group |
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