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Yorodumi- PDB-4x1k: Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modi... -
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-Basic information
Entry | Database: PDB / ID: 4x1k | ||||||
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Title | Discovery of cytotoxic Dolastatin 10 analogs with N-terminal modifications | ||||||
Components |
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Keywords | 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 | Function and homology information 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 / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Parris, K.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x1k.cif.gz | 383 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x1k.ent.gz | 302.6 KB | Display | PDB format |
PDBx/mmJSON format | 4x1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x1k_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 4x1k_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 4x1k_validation.xml.gz | 68.1 KB | Display | |
Data in CIF | 4x1k_validation.cif.gz | 90.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/4x1k ftp://data.pdbj.org/pub/pdb/validation_reports/x1/4x1k | HTTPS FTP |
-Related structure data
Related structure data | 4x1iC 4x1yC 4x20C 3hkbS 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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1 |
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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) Ovis aries (sheep) / References: UniProt: D0VWZ0 #2: Protein | Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9 #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.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043 |
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-Non-polymers , 5 types, 10 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 703.909 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H61N5O8 References: 2-methyl-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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 5% PEG 400, 0.1M LiSO4, 5-7% PEG 20K, 50 mM K-PIPES, pH 6.8 at 19oC |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 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: 3.5→50 Å / Num. obs: 26197 / % possible obs: 92.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 105.18 Å2 / Rmerge(I) obs: 0.153 / Χ2: 1.126 / Net I/av σ(I): 9.444 / Net I/σ(I): 3.9 / Num. measured all: 91138 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HKB Resolution: 3.5→45.45 Å / Cor.coef. Fo:Fc: 0.9158 / Cor.coef. Fo:Fc free: 0.9074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.696
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Displacement parameters | Biso mean: 144.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.777 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→45.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.64 Å / Total num. of bins used: 13
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