- PDB-5h7o: Crystal structure of DJ-101 in complex with tubulin protein -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5h7o
Title
Crystal structure of DJ-101 in complex with tubulin protein
Components
Stathmin-4
Tubulin alpha-1B chain
Tubulin beta-2B chain
Tubulin tyrosine ligase
Keywords
STRUCTURAL PROTEIN / DJ-101 / colchicine site tubulin inhibitor / tubulin / taxane resistance
Function / homology
Function and homology information
tubulin-tyrosine ligase activity / 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 ...tubulin-tyrosine ligase activity / 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 / positive regulation of axon guidance / 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 / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 6% poly(ethylene glycol) 4000, 8% glycerol, 0.1 M Mes, 30 mM CaCl2 and 30 mM MgCl2 (pH 6.7)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97853 Å / Relative weight: 1
Reflection
Resolution: 2.8→50 Å / Num. obs: 75002 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 19.3
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0135
refinement
HKL-3000
datareduction
HKL-3000
datascaling
MOLREP
phasing
Refinement
Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 15.309 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 2.516 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25623
3805
5.1 %
RANDOM
Rwork
0.21422
-
-
-
obs
0.21637
71085
99.78 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK