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- PDB-3zcw: Eg5 - New allosteric binding site -

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Basic information

Entry
Database: PDB / ID: 3zcw
TitleEg5 - New allosteric binding site
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsCELL CYCLE / INHIBITOR
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
Chem-4A2 / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.691 Å
AuthorsUlaganathan, V. / Talapatra, S.K. / Kozielski, F. / Pannifer, A.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Structural Insights Into a Unique Inhibitor Binding Pocket in Kinesin Spindle Protein.
Authors: Ulaganathan, V. / Talapatra, S.K. / Rath, O. / Pannifer, A.D. / Hackney, D.D. / Kozielski, F.
History
DepositionNov 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Structure summary
Revision 1.2Feb 27, 2013Group: Database references
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5227
Polymers38,8071
Non-polymers1,7156
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.940, 62.890, 75.050
Angle α, β, γ (deg.)90.00, 117.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

21A-2194-

HOH

31A-2203-

HOH

41A-2448-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein KINESIN-LIKE PROTEIN KIF11 / / 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: 38807.059 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 16-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODON PLUS / References: UniProt: P52732

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Non-polymers , 6 types, 456 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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-4A2 / (2E)-2-(3-fluoranyl-4-methoxy-phenyl)imino-1-[[2-(trifluoromethyl)phenyl]methyl]-3H-benzimidazole-5-carboxylic acid


Mass: 459.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H17F4N3O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.76 Å3/Da / Density % sol: 55.41 % / Description: NONE
Crystal growpH: 6.9
Details: 20% PEG3350, 2MM MAGNESIUM CHLORIDE, 100MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.69→36.96 Å / Num. obs: 49475 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 21.73 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOG

2wog


Resolution: 1.691→28.468 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2504 5.1 %
Rwork0.1941 --
obs0.196 49418 99.03 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.812 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.5704 Å20 Å2-3.116 Å2
2---0.0374 Å20 Å2
3---2.6078 Å2
Refinement stepCycle: LAST / Resolution: 1.691→28.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 113 450 3059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112743
X-RAY DIFFRACTIONf_angle_d1.4143750
X-RAY DIFFRACTIONf_dihedral_angle_d15.9651071
X-RAY DIFFRACTIONf_chiral_restr0.092435
X-RAY DIFFRACTIONf_plane_restr0.006469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.691-1.72350.29911440.30072543X-RAY DIFFRACTION98
1.7235-1.75870.28171420.27122556X-RAY DIFFRACTION99
1.7587-1.79690.31421350.25542649X-RAY DIFFRACTION100
1.7969-1.83870.30361480.24412609X-RAY DIFFRACTION99
1.8387-1.88470.27241430.26462592X-RAY DIFFRACTION99
1.8847-1.93570.40281390.35462578X-RAY DIFFRACTION99
1.9357-1.99260.25071350.24762607X-RAY DIFFRACTION99
1.9926-2.05690.22241370.17932621X-RAY DIFFRACTION100
2.0569-2.13040.21411260.18492623X-RAY DIFFRACTION99
2.1304-2.21570.26491410.19872609X-RAY DIFFRACTION99
2.2157-2.31640.33091540.27992581X-RAY DIFFRACTION99
2.3164-2.43850.21911440.18672593X-RAY DIFFRACTION100
2.4385-2.59120.23041620.17722617X-RAY DIFFRACTION100
2.5912-2.79110.26141360.18192621X-RAY DIFFRACTION99
2.7911-3.07170.24831380.17552619X-RAY DIFFRACTION99
3.0717-3.51550.1891290.16532638X-RAY DIFFRACTION99
3.5155-4.42640.19741150.15382612X-RAY DIFFRACTION97
4.4264-28.47210.16681360.172646X-RAY DIFFRACTION97

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