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- PDB-2x2r: Crystal structure of human kinesin Eg5 in complex with (R)-2-amin... -

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Basic information

Entry
Database: PDB / ID: 2x2r
TitleCrystal structure of human kinesin Eg5 in complex with (R)-2-amino-3-((4-chlorophenyl)diphenylmethylthio)propanoic acid
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsCELL CYCLE / MITOSIS / MICROTUBULE / ATP-BINDING / MOTOR PROTEIN / CELL DIVISION
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-X2O / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Structure-Activity Relationship and Multidrug Resistance Study of New S-Trityl-L-Cysteine Derivatives as Inhibitors of Eg5.
Authors: Kaan, H.Y.K. / Weiss, J. / Menger, D. / Ulaganathan, V. / Tkocz, K. / Laggner, C. / Popowycz, F. / Joseph, B. / Kozielski, F.
History
DepositionJan 15, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
B: KINESIN-LIKE PROTEIN KIF11
C: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,55212
Polymers123,1673
Non-polymers2,3859
Water13,277737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-65.9 kcal/mol
Surface area43380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 96.350, 124.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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 / KINESIN-LIKE PROTEIN 1 / TRIP-5


Mass: 41055.582 Da / Num. of mol.: 3 / 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 STAR (DE3) PLYSS / References: UniProt: P52732
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-X2O / (2R)-2-AMINO-3-[(2R)-2-METHYL-1,1-DIPHENYL-BUTYL]SULFANYL-PROPANOIC ACID / S-[(2R)-2-METHYL-1,1-DIPHENYLBUTYL]-L-CYSTEINE


Mass: 343.483 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H25NO2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.78 Å3/Da / Density % sol: 55.75 % / Description: NONE
Crystal growpH: 6
Details: 25% PEG3350, 0.15M SODIUM TARTRATE DIBASIC DIHYDRATE, 0.1M MES PH6.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 65550 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 33.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

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

1x88


Resolution: 2.2→29.411 Å / SU ML: 0.31 / σ(F): 0.05 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 3265 5.1 %
Rwork0.1724 --
obs0.1746 64602 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.819 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 37.96 Å2
Baniso -1Baniso -2Baniso -3
1-4.0793 Å20 Å20 Å2
2--4.0793 Å20 Å2
3----8.1586 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7717 0 156 737 8610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078089
X-RAY DIFFRACTIONf_angle_d1.11610985
X-RAY DIFFRACTIONf_dihedral_angle_d18.7523054
X-RAY DIFFRACTIONf_chiral_restr0.0761293
X-RAY DIFFRACTIONf_plane_restr0.0041393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.27890.26513410.18875906X-RAY DIFFRACTION96
2.2789-2.37010.24133390.1735979X-RAY DIFFRACTION97
2.3701-2.47790.26243200.186123X-RAY DIFFRACTION98
2.4779-2.60840.24513070.18316127X-RAY DIFFRACTION98
2.6084-2.77170.25633310.18156157X-RAY DIFFRACTION99
2.7717-2.98560.24483130.18176177X-RAY DIFFRACTION100
2.9856-3.28570.19663280.17656202X-RAY DIFFRACTION100
3.2857-3.76030.20583410.15876216X-RAY DIFFRACTION100
3.7603-4.73430.17473240.1416247X-RAY DIFFRACTION100
4.7343-29.41340.1923210.17696203X-RAY DIFFRACTION100

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