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Yorodumi- PDB-2uym: Crystal structure of KSP in complex with ADP and thiophene contai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uym | ||||||
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Title | Crystal structure of KSP in complex with ADP and thiophene containing inhibitor 37 | ||||||
Components | KINESIN-LIKE PROTEIN KIF11 | ||||||
Keywords | CELL CYCLE / KINESIN SPINDLE PROTEIN / KSP / EG5 / COMPLEX / INHIBITOR / THIOPHENE / ATP-BINDING / CELL DIVISION / COILED COIL / MICROTUBULE / MITOSIS / MOTOR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Lee, T.T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Synthesis and Sar of Thiophene Containing Kinesin Spindle Protein (Ksp) Inhibitors. Authors: Pinkerton, A.B. / Lee, T.T. / Hoffman, T.Z. / Wang, Y. / Kahraman, M. / Cook, T.G. / Severance, D. / Gahman, T.C. / Noble, S.A. / Shiau, A.K. / Davis, R.L. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uym.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uym.ent.gz | 120 KB | Display | PDB format |
PDBx/mmJSON format | 2uym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uym_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2uym_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2uym_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 2uym_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/2uym ftp://data.pdbj.org/pub/pdb/validation_reports/uy/2uym | HTTPS FTP |
-Related structure data
Related structure data | 2pg2C 2uyiC 1q0bS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-368 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52732 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | MOTOR PROTEIN NECESSARY FOR ESTABLISHI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
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Crystal grow | pH: 6 Details: 100 MM BIS-TRIS (PH 6.0), 200 MM AMMONIUM SULFATE AND 18-20% PEG3350. 10 MM SRCL2 |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 49950 / % possible obs: 99.6 % / Observed criterion σ(I): 1.8 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.8 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Q0B Resolution: 2.11→49.45 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.656 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→49.45 Å
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