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- PDB-4a51: Crystal structure of human kinesin Eg5 in complex with 1-(3-(((2-... -

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Basic information

Entry
Database: PDB / ID: 4a51
TitleCrystal structure of human kinesin Eg5 in complex with 1-(3-(((2-Aminoethyl)thio)diphenylmethyl)phenyl)ethanone hydrochloride
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsCELL CYCLE / MITOSIS / INHIBITOR / KSP
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / Kinesins / mitotic centrosome separation / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cell division / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / 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-DQ8 / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKaan, H.Y.K. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Triphenylbutanamines: Kinesin Spindle Protein Inhibitors with in Vivo Antitumor Activity.
Authors: Wang, F. / Good, J.A.D. / Rath, O. / Kaan, H.Y.K. / Sutcliffe, O.B. / Mackay, S.P. / Kozielski, F.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references / Other / Structure summary
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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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
D: KINESIN-LIKE PROTEIN KIF11
E: KINESIN-LIKE PROTEIN KIF11
F: KINESIN-LIKE PROTEIN KIF11
G: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,67343
Polymers287,3897
Non-polymers6,28336
Water4,053225
1
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0108
Polymers41,0561
Non-polymers9557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9396
Polymers41,0561
Non-polymers8845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9757
Polymers41,0561
Non-polymers9196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0367
Polymers41,0561
Non-polymers9806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9045
Polymers41,0561
Non-polymers8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9045
Polymers41,0561
Non-polymers8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9045
Polymers41,0561
Non-polymers8484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.840, 156.400, 170.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
KINESIN-LIKE PROTEIN KIF11 / EG5 / 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


Mass: 41055.582 Da / Num. of mol.: 7 / 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, 261 molecules

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


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-DQ8 / 1-(3-{[(2-aminoethyl)sulfanyl](diphenyl)methyl}phenyl)ethanone


Mass: 361.500 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C23H23NOS
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.37 Å3/Da / Density % sol: 63.53 % / Description: NONE
Crystal growpH: 5.8
Details: 22 % POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE, 0.1 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE AND 0.1 M MES PH 5.8

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.636
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.636 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 98930 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 58.62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X88

1x88


Resolution: 2.75→29.991 Å / SU ML: 0.78 / σ(F): 1.35 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 4934 5 %
Rwork0.2206 --
obs0.2237 98753 97.36 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.454 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 65.15 Å2
Baniso -1Baniso -2Baniso -3
1-19.8869 Å20 Å20 Å2
2---9.2658 Å20 Å2
3----10.6211 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17555 0 397 225 18177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318259
X-RAY DIFFRACTIONf_angle_d1.69924757
X-RAY DIFFRACTIONf_dihedral_angle_d18.7426826
X-RAY DIFFRACTIONf_chiral_restr0.1172901
X-RAY DIFFRACTIONf_plane_restr0.0083133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78120.38171590.33463048X-RAY DIFFRACTION96
2.7812-2.81390.41031380.33183084X-RAY DIFFRACTION96
2.8139-2.84820.351690.30483057X-RAY DIFFRACTION96
2.8482-2.88430.35621610.29353050X-RAY DIFFRACTION96
2.8843-2.92220.35181730.28093064X-RAY DIFFRACTION97
2.9222-2.96220.32241600.26243095X-RAY DIFFRACTION97
2.9622-3.00450.34451680.26023073X-RAY DIFFRACTION97
3.0045-3.04930.31351670.26193076X-RAY DIFFRACTION97
3.0493-3.09690.33891550.26513116X-RAY DIFFRACTION97
3.0969-3.14760.31191610.26113097X-RAY DIFFRACTION97
3.1476-3.20180.37081660.25863081X-RAY DIFFRACTION97
3.2018-3.25990.29791630.23593113X-RAY DIFFRACTION97
3.2599-3.32260.28981550.23153094X-RAY DIFFRACTION97
3.3226-3.39030.31590.22933113X-RAY DIFFRACTION98
3.3903-3.46390.30681670.2213127X-RAY DIFFRACTION98
3.4639-3.54440.28761560.21643116X-RAY DIFFRACTION98
3.5444-3.63290.2991600.21383135X-RAY DIFFRACTION97
3.6329-3.73090.28021820.20693102X-RAY DIFFRACTION98
3.7309-3.84050.29441590.21043143X-RAY DIFFRACTION98
3.8405-3.96420.24571660.20253151X-RAY DIFFRACTION98
3.9642-4.10550.25821620.18963147X-RAY DIFFRACTION98
4.1055-4.26950.26091840.17943171X-RAY DIFFRACTION99
4.2695-4.46320.23371570.1593190X-RAY DIFFRACTION99
4.4632-4.69760.19651540.15153187X-RAY DIFFRACTION99
4.6976-4.99070.21131650.17053207X-RAY DIFFRACTION99
4.9907-5.3740.2851920.20493168X-RAY DIFFRACTION99
5.374-5.91110.28031820.22463192X-RAY DIFFRACTION98
5.9111-6.75790.30161620.2423225X-RAY DIFFRACTION98
6.7579-8.48220.23521510.19773246X-RAY DIFFRACTION98
8.4822-29.99270.29241810.29163151X-RAY DIFFRACTION92

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