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- PDB-4bxn: Eg5(WT) complex -

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Basic information

Entry
Database: PDB / ID: 4bxn
TitleEg5(WT) complex
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsMOTOR PROTEIN / MITOSIS
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
Chem-6LX / ADENOSINE-5'-DIPHOSPHATE / : / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.793 Å
AuthorsTalapatra, S.K. / Anthony, N.G. / Mackay, S.P. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: The Mitotic Kinesin Eg5 Overcomes Inhibition to the Phase I/II Clinical Candidate Sb743921 by an Allosteric Resistance Mechanism.
Authors: Talapatra, S.K. / Anthony, N.G. / Mackay, S.P. / Kozielski, F.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 17, 2014Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.4Mar 8, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,75636
Polymers82,1112
Non-polymers4,64534
Water1,04558
1
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,18917
Polymers41,0561
Non-polymers2,13316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56819
Polymers41,0561
Non-polymers2,51218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.426, 81.426, 115.202
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 , 1 types, 2 molecules AB

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


Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-368
Source method: isolated from a genetically manipulated source
Details: SB743921 AS A LIGAND / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: P52732

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Non-polymers , 5 types, 92 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-6LX / N-(3-aminopropyl)-N-[(1R)-1-(3-benzyl-7-chloro-4-oxo-4H-chromen-2-yl)-2-methylpropyl]-4-methylbenzamide


Mass: 517.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H33ClN2O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 20

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.23 % / Description: NONE
Crystal growpH: 6.8
Details: 0.02 M CACL2, 0.02 M CADMIUM CHLORIDE, 0.02 M COBALT(II) CHLORIDE, 20% W/V PEG-3350, pH 6.8

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.8→30 Å / Num. obs: 9633 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 83.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6
Reflection shellResolution: 3→30 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
CCP4SUITEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AS7

4as7


Resolution: 2.793→27.935 Å / σ(F): 1.96 / Phase error: 34.63 / Stereochemistry target values: TWIN_LSQ_F
Details: DISORDERED REGION EITHER DELETED OR MODELLED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.274 1087 5.3 %
Rwork0.2302 --
obs0.2333 9633 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.9 Å2
Refinement stepCycle: LAST / Resolution: 2.793→27.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 158 58 5521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015552
X-RAY DIFFRACTIONf_angle_d1.5877527
X-RAY DIFFRACTIONf_dihedral_angle_d22.3782065
X-RAY DIFFRACTIONf_chiral_restr0.099879
X-RAY DIFFRACTIONf_plane_restr0.006954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7997-2.9270.41771320.38042406X-RAY DIFFRACTION91
2.927-3.08110.3511500.34642385X-RAY DIFFRACTION90
3.0811-3.27390.37091200.32362510X-RAY DIFFRACTION95
3.2739-3.52620.34261440.30052487X-RAY DIFFRACTION94
3.5262-3.88020.34891250.27742438X-RAY DIFFRACTION93
3.8802-4.43980.27581230.2232391X-RAY DIFFRACTION91
4.4398-5.58630.23831270.20072469X-RAY DIFFRACTION95
5.5863-27.93650.20761380.16482434X-RAY DIFFRACTION92

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