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- PDB-4x1y: Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4x1y | ||||||
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Title | Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications | ||||||
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![]() | Structural Protein/Inhibitor / Binding Sites / Competitive / Cattle / Tumor / Colchicine / Humans / Microtubules / Protein Binding / Protein Conformation / Protein Multimerization / Tubulin / Tubulin Modulators / Structural Protein-Inhibitor complex | ||||||
Function / homology | ![]() axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / cerebral cortex development / memory / cytoplasmic ribonucleoprotein granule / microtubule cytoskeleton organization / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Parris, K.D. | ||||||
![]() | ![]() Title: Discovery of cytotoxic dolastatin 10 analogues with N-terminal modifications. Authors: Maderna, A. / Doroski, M. / Subramanyam, C. / Porte, A. / Leverett, C.A. / Vetelino, B.C. / Chen, Z. / Risley, H. / Parris, K. / Pandit, J. / Varghese, A.H. / Shanker, S. / Song, C. / ...Authors: Maderna, A. / Doroski, M. / Subramanyam, C. / Porte, A. / Leverett, C.A. / Vetelino, B.C. / Chen, Z. / Risley, H. / Parris, K. / Pandit, J. / Varghese, A.H. / Shanker, S. / Song, C. / Sukuru, S.C. / Farley, K.A. / Wagenaar, M.M. / Shapiro, M.J. / Musto, S. / Lam, M.H. / Loganzo, F. / O'Donnell, C.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 | ![]() | 382.8 KB | Display | ![]() |
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PDB format | ![]() | 302.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 66.8 KB | Display | |
Data in CIF | ![]() | 89.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x1iC ![]() 4x1kC ![]() 4x20C ![]() 3hkbS C: citing same article ( 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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Unit cell |
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Components
-Protein , 3 types, 5 molecules ACBDE
#1: Protein | Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Protein | Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 16719.938 Da / Num. of mol.: 1 / Fragment: UNP residues 49-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 10 molecules ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/LOC.gif)
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![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/LOC.gif)
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#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ![]() References: N,2-dimethyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 5% PEG 400, 0.1M LiSO4, 5-7% PEG 20K, 50 mM K-PIPES |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.19→50 Å / Num. obs: 36225 / % possible obs: 97.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 94.19 Å2 / Rmerge(I) obs: 0.104 / Χ2: 0.842 / Net I/av σ(I): 14.559 / Net I/σ(I): 4.7 / Num. measured all: 164538 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HKB Resolution: 3.19→30.59 Å / Cor.coef. Fo:Fc: 0.9218 / Cor.coef. Fo:Fc free: 0.8849 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.548
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Displacement parameters | Biso mean: 126.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.737 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.19→30.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.19→3.28 Å / Total num. of bins used: 18
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