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Open data
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Basic information
Entry | Database: PDB / ID: 1wq8 | |||||||||
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Title | Crystal structure of Vammin, a VEGF-F from a snake venom | |||||||||
![]() | Vascular endothelial growth factor toxin | |||||||||
![]() | TOXIN / snake venom / Vascular endothelial growth factor / VEGF / VEGF-F | |||||||||
Function / homology | ![]() growth factor activity / toxin activity / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H. | |||||||||
![]() | ![]() Title: Crystal structures of novel vascular endothelial growth factors (VEGF) from snake venoms: insight into selective VEGF binding to kinase insert domain-containing receptor but not to fms-like tyrosine kinase-1. Authors: Suto, K. / Yamazaki, Y. / Morita, T. / Mizuno, H. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Snake venom vascular endothelial growth factors (VEGFs) exhibit potent activity through their specific recognition of KDR (VEGF receptor 2) Authors: Yamazaki, Y. / Takani, K. / Atoda, H. / Morita, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.5 KB | Display | ![]() |
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PDB format | ![]() | 25.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis:y, x, -z |
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Components
#1: Protein | Mass: 12575.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: PEG 6000, Tris-HCl, glycerol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2003 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 13068 / Num. obs: 12903 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.218 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: VR-1 Resolution: 1.9→23 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1706273.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.5954 Å2 / ksol: 0.377209 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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