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- PDB-4a50: Crystal structure of human kinesin Eg5 in complex with 2-Amino-5-... -

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Basic information

Entry
Database: PDB / ID: 4a50
TitleCrystal structure of human kinesin Eg5 in complex with 2-Amino-5-(3-methylphenyl)-5,5-diphenylpentanoic acid
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-DQ6 / Chem-DQ7 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2265
Polymers41,0561
Non-polymers1,1704
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.540, 158.540, 158.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / EG5 / KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HK KINESIN-RELATED MOTOR PROTEIN EG5 / ...EG5 / KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HK KINESIN-RELATED MOTOR PROTEIN EG5 / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5


Mass: 41055.582 Da / Num. of mol.: 1 / 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 , 5 types, 42 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-DQ6 / (2S)-2-AMINO-5-(3-METHYLPHENYL)-5,5-DIPHENYLPROPANOIC ACID


Mass: 359.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25NO2
#5: Chemical ChemComp-DQ7 / (2R)-2-AMINO-5-(3-METHYLPHENYL)-5,5-DIPHENYLPROPANOIC ACID


Mass: 359.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 4.06 Å3/Da / Density % sol: 69.69 % / Description: NONE
Crystal growpH: 5.5
Details: 23 % POLYETHYLENE GLYCOL-3350, 0.25 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 17322 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KEN

3ken


Resolution: 2.75→28.03 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.256 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24301 890 5.2 %RANDOM
Rwork0.19759 ---
obs0.19989 16381 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.825 Å2
Refinement stepCycle: LAST / Resolution: 2.75→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 0 82 38 2720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222725
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7472.0033698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9124.248113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.48515473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751519
X-RAY DIFFRACTIONr_chiral_restr0.1170.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212006
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2241.51681
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34422729
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.13731044
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3874.5969
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.752→2.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 85 -
Rwork0.283 1174 -
obs--99.76 %

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