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Open data
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Basic information
Entry | Database: PDB / ID: 1dy2 | ||||||
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Title | Murine collagen alpha1(XV), endostatin domain | ||||||
![]() | COLLAGEN ALPHA1(XV) CHAIN | ||||||
![]() | ANGIOGENESIS INHIBITOR | ||||||
Function / homology | ![]() Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / endothelial cell morphogenesis / collagen trimer / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / extracellular matrix ...Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / endothelial cell morphogenesis / collagen trimer / extracellular matrix structural constituent / basement membrane / extracellular matrix organization / extracellular matrix / angiogenesis / collagen-containing extracellular matrix / cell adhesion / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tisi, D. / Hohenester, E. / Sasaki, T. / Timpl, R. | ||||||
![]() | ![]() Title: Endostatin Derived from Collagens Xv and Xviii Differ in Structural and Binding Properties, Tissue Distribution and Anti-Angiogenic Activity Authors: Sasaki, T. / Larsson, H. / Tisi, D. / Claesson-Welsh, L. / Hohenester, E. / Timpl, R. #1: ![]() Title: Crystal Structure of the Angiogenesis Inhibitor Endostatin at 1.5 Angstrom Resolution Authors: Hohenester, E. / Sasaki, T. / Olsen, B.R. / Timpl, R. #2: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Endostatin: An Endogenous Inhibitor of Angiogenesis and Tumor Growth Authors: O'Reilly, M.S. / Boehm, T. / Shing, Y. / Fukai, N. / Vasios, G. / Lane, W.S. / Flynn, E. / Birkhead, J.R. / Olsen, B.R. / Folkman, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.6 KB | Display | ![]() |
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PDB format | ![]() | 32.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1koeS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | BIOLOGICAL UNIT IS A MONOMER |
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Components
#1: Protein | Mass: 20085.875 Da / Num. of mol.: 1 / Fragment: ENDOSTATIN DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Sequence details | N-TERMINAL APLA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 9225 / % possible obs: 97.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.152 / % possible all: 97.2 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KOE Resolution: 2→20 Å / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |