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- PDB-1x88: Human Eg5 motor domain bound to Mg-ADP and monastrol -

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Basic information

Entry
Database: PDB / ID: 1x88
TitleHuman Eg5 motor domain bound to Mg-ADP and monastrol
ComponentsKinesin-like protein KIF11
KeywordsCELL CYCLE / Switch II / Motor domain / Neck linker
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 / Chem-NAT / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMaliga, Z. / Mitchison, T.J.
CitationJournal: TO BE PUBLISHED
Title: Structural Basis of Eg5 Inhibition by Monastrol
Authors: Maliga, Z. / Mitchison, T.J.
History
DepositionAug 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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)81,8518
Polymers80,3632
Non-polymers1,4886
Water12,574698
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9264
Polymers40,1821
Non-polymers7443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9264
Polymers40,1821
Non-polymers7443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.706, 79.648, 159.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / TRIP5 / Kinesin-like protein 1


Mass: 40181.652 Da / Num. of mol.: 2 / Fragment: Kinesin-motor
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, KNSL1, EG5 / Plasmid: pRSETa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P52732
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-NAT / ETHYL 4-(3-HYDROXYPHENYL)-6-METHYL-2-THIOXO-1,2,3,4-TETRAHYDROPYRIMIDINE-5-CARBOXYLATE / MONASTROL / Monastrol


Mass: 292.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O3S / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 275 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: PEG3350, ammonium tartrate, potassium chloride, adenosine diphosphate, monastrol, sodium azide, PIPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 275K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.9641, 0.9794, 0.9797
SYNCHROTRONALS 8.2.120.9919
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 12, 2003
ADSC QUANTUM 2102CCDDec 12, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96411
20.97941
30.97971
40.99191
ReflectionResolution: 1.7→20 Å / Num. all: 98099 / Num. obs: 93881 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 13.4 Å2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / % possible all: 73.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: Chain building into electron density map obtained from Solve using MAD

Resolution: 1.8→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 291975.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 8076 10 %RANDOM
Rwork0.203 ---
all0.205 82941 --
obs0.203 80785 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0124 Å2 / ksol: 0.365705 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2---1.13 Å20 Å2
3---2.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5237 0 96 698 6031
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.432
X-RAY DIFFRACTIONc_scangle_it3.592.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 1255 10.4 %
Rwork0.223 10864 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3ADP.PARAMADP.TOP
X-RAY DIFFRACTION4S_MONASTROL.PARAMS_MONASTROL.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMWATER.TOP

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