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- PDB-2gm1: Crystal structure of the mitotic kinesin eg5 in complex with mg-a... -

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Basic information

Entry
Database: PDB / ID: 2gm1
TitleCrystal structure of the mitotic kinesin eg5 in complex with mg-adp and n-(3-aminopropyl)-n-((3-benzyl-5-chloro-4-oxo-3,4-dihydropyrrolo[2,1-f][1,2,4]triazin-2-yl)(cyclopropyl)methyl)-4-methylbenzamide
ComponentsKINESIN-RELATED MOTOR PROTEIN EG5
KeywordsCELL CYCLE / Eg5 Mg-ADP Complex Inhibitor
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / Kinesins / mitotic centrosome separation / plus-end-directed microtubule motor activity / 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 / mitotic centrosome separation / plus-end-directed microtubule motor activity / 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 profile. / Kinesin motor, catalytic domain. ATPase. ...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 profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2AZ / ADENOSINE-5'-DIPHOSPHATE / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.3 Å
AuthorsSheriff, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Synthesis and SAR of pyrrolotriazine-4-one based Eg5 inhibitors.
Authors: Kim, K.S. / Lu, S. / Cornelius, L.A. / Lombardo, L.J. / Borzilleri, R.M. / Schroeder, G.M. / Sheng, C. / Rovnyak, G. / Crews, D. / Schmidt, R.J. / Williams, D.K. / Bhide, R.S. / Traeger, S.C. ...Authors: Kim, K.S. / Lu, S. / Cornelius, L.A. / Lombardo, L.J. / Borzilleri, R.M. / Schroeder, G.M. / Sheng, C. / Rovnyak, G. / Crews, D. / Schmidt, R.J. / Williams, D.K. / Bhide, R.S. / Traeger, S.C. / McDonnell, P.A. / Mueller, L. / Sheriff, S. / Newitt, J.A. / Pudzianowski, A.T. / Yang, Z. / Wild, R. / Lee, F.Y. / Batorsky, R. / Ryder, J.S. / Ortega-Nanos, M. / Shen, H. / Gottardis, M. / Roussell, D.L.
History
DepositionApr 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-RELATED MOTOR PROTEIN EG5
B: KINESIN-RELATED MOTOR PROTEIN EG5
D: KINESIN-RELATED MOTOR PROTEIN EG5
E: KINESIN-RELATED MOTOR PROTEIN EG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,14220
Polymers164,2224
Non-polymers3,91916
Water4,252236
1
A: KINESIN-RELATED MOTOR PROTEIN EG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0355
Polymers41,0561
Non-polymers9804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KINESIN-RELATED MOTOR PROTEIN EG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0355
Polymers41,0561
Non-polymers9804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: KINESIN-RELATED MOTOR PROTEIN EG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0355
Polymers41,0561
Non-polymers9804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: KINESIN-RELATED MOTOR PROTEIN EG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0355
Polymers41,0561
Non-polymers9804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 112.600, 108.100
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
KINESIN-RELATED MOTOR PROTEIN EG5


Mass: 41055.582 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EG5 / Plasmid: PET 43D / 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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-2AZ / N-(3-AMINOPROPYL)-N-[(R)-(3-BENZYL-5-CHLORO-4-OXO-3,4-DIHYDROPYRROLO[2,1-F][1,2,4]TRIAZIN-2-YL)(CYCLOPROPYL)METHYL]-4-METHYLBENZAMIDE


Mass: 504.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H30ClN5O2
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 277 K / pH: 7.5
Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.5, 0.2 M MgCl2, 28% (v/v) PEG-3350; protein: 3.69 mg/ml (90 uM) in 20 mM PIPES pH 6.8, 2 mM MgCl2, 1 mM EGTA, 25 mM DTT, 478 uM ADP, 478 uM BMS-607205, 1.0% ...Details: 1:1 reservoir: 0.1 M NaHEPES pH 7.5, 0.2 M MgCl2, 28% (v/v) PEG-3350; protein: 3.69 mg/ml (90 uM) in 20 mM PIPES pH 6.8, 2 mM MgCl2, 1 mM EGTA, 25 mM DTT, 478 uM ADP, 478 uM BMS-607205, 1.0% DMSO , pH 7.8, 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
DetectorType: ADSC / Detector: CCD / Date: Jun 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Av σ(I) over netI: 11.4 / Number: 254796 / Rmerge(I) obs: 0.067 / Χ2: 1.04 / D res high: 2.3 Å / D res low: 50 Å / Num. obs: 67500 / % possible obs: 99.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.9550685299.40.0391.0533.7
3.934.9568091000.0420.9893.8
3.443.9367871000.0530.9913.8
3.123.4467711000.0661.1473.8
2.93.1267591000.0851.0583.8
2.732.967241000.1111.0563.8
2.592.73674199.90.151.0963.8
2.482.59670099.50.1841.0283.7
2.382.48669799.10.2270.9983.7
2.32.38666099.10.2710.9583.7
ReflectionResolution: 2.3→50 Å / Num. obs: 67500 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 5.1 / % possible all: 99.1

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Phasing

Phasing MRRfactor: 0.384 / Cor.coef. Fo:Fc: 0.652 / Cor.coef. Io to Ic: 0.682
Highest resolutionLowest resolution
Translation4 Å10 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
CNX2005refinement
RefinementMethod to determine structure: molecular replacement
Starting model: EG5 TETRAMER

Resolution: 2.3→49.86 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1956724.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue ...Details: Due to a feature in the refinement program, the structure was refined with an OXT on a residue that is not the terminal residue of the sequence. The OXT was changed to N of the next residue by the wwPDB annotation staff.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 821 1.2 %RANDOM
Rwork0.23 ---
all-67477 --
obs-67477 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.409 Å2 / ksol: 0.369911 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å23.72 Å2
2--5.55 Å20 Å2
3----4.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9947 0 260 236 10443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.092.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION3.050.222125
22X-RAY DIFFRACTION3.050.222125
33X-RAY DIFFRACTION2.470.282125
44X-RAY DIFFRACTION3.60.382125
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3 101 1.4 %
Rwork0.251 7286 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION42AZ.PARADP.TOP
X-RAY DIFFRACTION5ADP.PAR2AZ.TOP

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