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- PDB-2v4b: Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v4b | ||||||
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Title | Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (apo-form) | ||||||
![]() | ADAMTS-1 | ||||||
![]() | HYDROLASE / ZYMOGEN / PROTEASE / ADAMTS-1 / METALLOPROTEASE / HEPARIN-BINDING / METALLOPROTEINASE / METZINCIN / GLYCOPROTEIN / METAL-BINDING / EXTRACELLULAR MATRIX / CLEAVAGE ON PAIR OF BASIC RESIDUES | ||||||
Function / homology | ![]() 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 / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix ...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 / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / negative regulation of angiogenesis / extracellular matrix organization / extracellular matrix / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gerhardt, S. / Hassall, G. / Hawtin, P. / McCall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M. | ||||||
![]() | ![]() Title: Crystal Structures of Human Adamts-1 Reveal a Conserved Catalytic Domain and a Disintegrin-Like Domain with a Fold Homologous to Cysteine-Rich Domains. Authors: Gerhardt, S. / Hassall, G. / Hawtin, P. / Mccall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.3 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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 oper: (Code: given Matrix: (0.02465, 0.02414), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32911.938 Da / Num. of mol.: 2 Fragment: CATALYTIC DOMAIN INCL. CYSTEINE-RICH DOMAIN, RESIDUES 253-548 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UHI8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Non-polymers , 6 types, 241 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-NI / #5: Chemical | #6: Chemical | ChemComp-NA / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | CLEAVES AGGRECAN, A CARTILAGE PROTEOGLYC |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.06 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.2-0.6M SODIUM ACETATE, 0.05M CADMIUM SULPHATE, 0.1M HEPES PH 7.0, 12-22% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→40.26 Å / Num. obs: 50457 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.64 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.17 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 421-427 AND 433-437 ARE DISORDERED
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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 mean: 35.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.26 Å
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Refine LS restraints |
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