+Open data
-Basic information
Entry | Database: PDB / ID: 7tte | ||||||
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Title | Tubulin-RB3_SLD in complex with compound 12j | ||||||
Components |
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Keywords | CELL CYCLE/INHIBITOR / MICROTUBULE INHIBITOR / COLCHICINE / CELL CYCLE / CANCER / INHIBITOR COMPLEX / CELL CYCLE-INHIBITOR complex | ||||||
Function / homology | Function and homology information Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / growth cone / microtubule / neuron projection / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | White, S.W. / Yun, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Pharmacol Transl Sci / Year: 2023 Title: Design, Synthesis, and Biological Evaluation of Pyrimidine Dihydroquinoxalinone Derivatives as Tubulin Colchicine Site-Binding Agents That Displayed Potent Anticancer Activity Both In Vitro and In Vivo. Authors: Pochampally, S. / Hartman, K.L. / Wang, R. / Wang, J. / Yun, M.K. / Parmar, K. / Park, H. / Meibohm, B. / White, S.W. / Li, W. / Miller, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tte.cif.gz | 891.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tte.ent.gz | 619.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tte_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7tte_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7tte_validation.xml.gz | 63.9 KB | Display | |
Data in CIF | 7tte_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tte ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tte | HTTPS FTP |
-Related structure data
Related structure data | 7ttdC 7ttfC 6xesS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 48780.117 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4 #2: Protein | Mass: 48648.652 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7 #3: Protein | | Mass: 16851.133 Da / Num. of mol.: 1 / Mutation: C14A, F20W 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 , 6 types, 23 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GDP / | #7: Chemical | #8: Chemical | ChemComp-MG / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.6 Details: 0.2M ammonium sulfate, 0.1 M tri-sodium citrate, pH 5.6, 14 % PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 56674 / % possible obs: 95.5 % / Redundancy: 24.3 % / Biso Wilson estimate: 80.13 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.025 / Rrim(I) all: 0.127 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 20 % / Rmerge(I) obs: 1.399 / Num. unique obs: 3831 / CC1/2: 0.865 / CC star: 0.963 / Rpim(I) all: 0.282 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XES Resolution: 2.7→45.12 Å / SU ML: 0.4061 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.3019 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→45.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 9.43266939167 Å / Origin y: 24.8971914347 Å / Origin z: 29.7294660782 Å
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Refinement TLS group | Selection details: all |