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- PDB-3ken: Human Eg5 in complex with S-trityl-L-cysteine -

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Basic information

Entry
Database: PDB / ID: 3ken
TitleHuman Eg5 in complex with S-trityl-L-cysteine
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / cell cycle / kinesin-inhibitor complex / motor domain / L5 loop / ATP-binding / Cell division / Coiled coil / Microtubule / Mitosis / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / N,N-dimethylmethanamine / S-TRITYL-L-CYSTEINE / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsParke, C.L. / Wojcik, E.J. / Kim, S. / Worthylake, D.K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Allosteric drug discrimination is coupled to mechanochemical changes in the kinesin-5 motor core.
Authors: Kim, E.D. / Buckley, R. / Learman, S. / Richard, J. / Parke, C. / Worthylake, D.K. / Wojcik, E.J. / Walker, R.A. / Kim, S.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0435
Polymers41,1691
Non-polymers8744
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.930, 157.930, 157.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Kinesin-like protein KIF11 / / Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor- ...Kinesin-related motor protein Eg5 / Kinesin-like spindle protein HKSP / Thyroid receptor-interacting protein 5 / TRIP-5 / Kinesin-like protein 1


Mass: 41168.738 Da / Num. of mol.: 1
Fragment: motor domain of human kinesin Eg5 (residues 1-369)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EG5, KIF11, KNSL1, TRIP5 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52732

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZZD / S-TRITYL-L-CYSTEINE


Type: L-peptide linking / Mass: 363.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21NO2S
#4: Chemical ChemComp-KEN / N,N-dimethylmethanamine / Trimethylamine


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 3.99 Å3/Da / Density % sol: 69.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 250 mM NH4SO4, 100 mM MES pH 6.0, 25% PEG 3350, 5-15% glycerol, 10 mM trimethylamine, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 13, 2008
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→28.78 Å / Num. all: 22685 / Num. obs: 22664 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.92 % / Biso Wilson estimate: 33.341 Å2 / Rsym value: 0.1188 / Net I/σ(I): 14.18
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.15 % / Mean I/σ(I) obs: 2.89 / Num. unique all: 2265 / Rsym value: 0.5101 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1X88 molecule A

1x88


Resolution: 2.5→25 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2232 9.8 %random
Rwork0.241 ---
all-22501 --
obs-20269 98.7 %-
Solvent computationBsol: 20.597 Å2
Displacement parametersBiso max: 74.35 Å2 / Biso mean: 25.379 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 58 74 2749
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.610.34192790.3059X-RAY DIFFRACTION2642
2.61-2.750.31292710.2866X-RAY DIFFRACTION2805
2.75-2.920.32882970.2943X-RAY DIFFRACTION2809
2.92-3.150.34862770.2797X-RAY DIFFRACTION2815
3.15-3.460.29062620.2583X-RAY DIFFRACTION2808
3.46-3.960.24092870.2253X-RAY DIFFRACTION2816
3.96-4.990.20972860.1815X-RAY DIFFRACTION2854
4.99-250.25522730.2154X-RAY DIFFRACTION2952
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2adp.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4origstc.param
X-RAY DIFFRACTION5trimethylamine.param
X-RAY DIFFRACTION6CNS_TOPPAR:ion.param

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