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- PDB-2fl2: crystal structure of KSP in complex with inhibitor 19 -

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Basic information

Entry
Database: PDB / ID: 2fl2
Titlecrystal structure of KSP in complex with inhibitor 19
ComponentsKinesin-like protein KIF11
KeywordsCELL CYCLE / KSP / KSP-inhibitor complex
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle pole / spindle / 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-N4T / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsYan, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Kinesin spindle protein (KSP) inhibitors. Part 2: the design, synthesis, and characterization of 2,4-diaryl-2,5-dihydropyrrole inhibitors of the mitotic kinesin KSP.
Authors: Fraley, M.E. / Garbaccio, R.M. / Arrington, K.L. / Hoffman, W.F. / Tasber, E.S. / Coleman, P.J. / Buser, C.A. / Walsh, E.S. / Hamilton, K. / Fernandes, C. / Schaber, M.D. / Lobell, R.B. / ...Authors: Fraley, M.E. / Garbaccio, R.M. / Arrington, K.L. / Hoffman, W.F. / Tasber, E.S. / Coleman, P.J. / Buser, C.A. / Walsh, E.S. / Hamilton, K. / Fernandes, C. / Schaber, M.D. / Lobell, R.B. / Tao, W. / South, V.J. / Yan, Y. / Kuo, L.C. / Prueksaritanont, T. / Shu, C. / Torrent, M. / Heimbrook, D.C. / Kohl, N.E. / Huber, H.E. / Hartman, G.D.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
Remark 999SEQUENCE Met at position 1 was cleaved during purification

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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)83,4618
Polymers81,8492
Non-polymers1,6126
Water2,324129
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7304
Polymers40,9241
Non-polymers8063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7304
Polymers40,9241
Non-polymers8063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.8, 79.5, 159.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Detailsthis motor domain is a part of multi-domain protien that forms a tetramer, there are two monomers in an asymetric unit.

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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: 40924.387 Da / Num. of mol.: 2 / Fragment: Kinesin-motor domain, residues 1-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1 / 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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-N4T / (1S)-1-CYCLOPROPYL-2-[(2S)-4-(2,5-DIFLUOROPHENYL)-2-PHENYL-2,5-DIHYDRO-1H-PYRROL-1-YL]-2-OXOETHANAMINE


Mass: 354.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20F2N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: peg3350, potassium phosphate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 35310 / Num. obs: 18467 / % possible obs: 53 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 12
Reflection shellResolution: 2.48→2.57 Å / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1133 / Rsym value: 0.336 / % possible all: 32

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1613 -random
Rwork0.257 ---
all0.26 30915 --
obs0.26 14627 53 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 108 129 5425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0162
X-RAY DIFFRACTIONc_angle_deg2.11

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