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- PDB-2xae: Crystal structure of human kinesin Eg5 in complex with (R)-2-amin... -

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Basic information

Entry
Database: PDB / ID: 2xae
TitleCrystal structure of human kinesin Eg5 in complex with (R)-2-amino-3-((S)-2-methyl-1,1-diphenylbutylthio)propanoic acid
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsCELL CYCLE / MITOSIS / KSP
Function / homology
Function and homology information


Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / ATP-dependent microtubule motor activity, plus-end-directed / regulation of mitotic centrosome separation / mitotic centrosome separation / kinesin complex / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / microtubule motor activity / spindle organization ...Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / ATP-dependent microtubule motor activity, plus-end-directed / regulation of mitotic centrosome separation / mitotic centrosome separation / kinesin complex / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / antigen processing and presentation of exogenous peptide antigen via MHC class II / mitotic spindle organization / mitotic spindle / spindle microtubule / spindle / spindle pole / mitotic cell cycle / microtubule / microtubule binding / ATPase activity / cell division / protein kinase binding / protein-containing complex / membrane / ATP binding / nucleus / cytosol
Kinesin motor domain / Kinesin-associated microtubule-binding / Kinesin motor domain superfamily / Kinesin-like protein / P-loop containing nucleoside triphosphate hydrolase / Kinesin-associated microtubule-binding domain / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain signature. / Kinesin motor domain profile.
Kinesin-like protein KIF11
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Tkocz, K. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Structure-Activity Relationship and Multidrug Resistance Study of New S-Trityl-L-Cysteine Derivatives as Inhibitors of Eg5.
Authors: Kaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Tkocz, K. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 31, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF11
B: KINESIN-LIKE PROTEIN KIF11
C: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,03916
Polymers123,1673
Non-polymers2,87213
Water6,593366
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-111.6 kcal/mol
Surface area43440 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)96.770, 96.770, 124.751
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein/peptide , 1 types, 3 molecules ABC

#1: Protein/peptide KINESIN-LIKE PROTEIN KIF11 / EG5 / KINESIN-RELATED MOTOR PROTEIN EG5 / KINESIN-LIKE SPINDLE PROTEIN HKSP / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5 / KINESIN-LIKE PROTEIN 1


Mass: 41055.582 Da / Num. of mol.: 3 / Fragment: MOTOR 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) / Variant (production host): PLYSS / References: UniProt: P52732

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Non-polymers , 6 types, 379 molecules

#2: Chemical ChemComp-2XA / (2R)-2-AMINO-3-[(4-CHLOROPHENYL)-DIPHENYL-METHYL]SULFANYL-PROPANOIC ACID


Mass: 397.918 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H20ClNO2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Chloride
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.17 % / Description: NONE
Crystal growpH: 6
Details: 24% POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE, 0.01 M TRIMETHYLAMINE HYDROCHLORIDE AND 0.1 M MES PH 6.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 40212 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 57.22 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOG
Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.596 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.627 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25708 2013 5 %RANDOM
Rwork0.1814 ---
Obs0.18512 38172 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.505 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 181 366 8225
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0130.0228084
r_bond_other_d
r_angle_refined_deg1.8321.99510978
r_angle_other_deg
r_dihedral_angle_1_deg6.87851007
r_dihedral_angle_2_deg37.76623.971345
r_dihedral_angle_3_deg18.222151445
r_dihedral_angle_4_deg18.5871561
r_chiral_restr0.1170.21283
r_gen_planes_refined0.0070.0215943
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it1.0671.54961
r_mcbond_other
r_mcangle_it2.05328072
r_mcangle_other
r_scbond_it2.98133123
r_scbond_other
r_scangle_it5.2164.52892
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 146 -
Rwork0.277 2849 -
Obs--100 %

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