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- PDB-3k3b: Co-crystal structure of the human kinesin Eg5 with a novel tetrah... -

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Basic information

Entry
Database: PDB / ID: 3k3b
TitleCo-crystal structure of the human kinesin Eg5 with a novel tetrahydro-beta-carboline
ComponentsKinesin-like protein KIF11
KeywordsMOTOR PROTEIN / protein-ligand complex / ATP-binding / Cell cycle / Cell division / Microtubule / Mitosis / Nucleotide-binding / Phosphoprotein
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-L31 / NITRATE ION / DI(HYDROXYETHYL)ETHER / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBussiere, D.E. / Bellamacina, C. / Le, V.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: The discovery of tetrahydro-beta-carbolines as inhibitors of the kinesin Eg5.
Authors: Barsanti, P.A. / Wang, W. / Ni, Z.J. / Duhl, D. / Brammeier, N. / Martin, E. / Bussiere, D. / Walter, A.O.
History
DepositionOct 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 13, 2013Group: Refinement description
Revision 1.3Feb 21, 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.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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,92112
Polymers82,1112
Non-polymers1,80910
Water5,567309
1
A: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0317
Polymers41,0561
Non-polymers9756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-like protein KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8895
Polymers41,0561
Non-polymers8344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-43 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.970, 92.670, 102.950
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, 2 molecules AB

#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 / TRIP-5 / Kinesin-like protein 1


Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: P52732

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Non-polymers , 7 types, 319 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-L31 / 3-[(1R)-2-acetyl-6-methyl-2,3,4,9-tetrahydro-1H-beta-carbolin-1-yl]phenol


Mass: 320.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20N2O2
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15-17% PEG3350 150-300 mM NaNO3 100 mM MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.953724 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2.4→39.96 Å / Num. all: 30120 / Num. obs: 29909 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4344 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
EPMRphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→39.96 Å / SU ML: 2.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 1419 4.98 %random
Rwork0.2055 ---
all0.2075 30120 --
obs0.2075 28490 99.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.008 Å2 / ksol: 0.34 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5147 0 120 309 5576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075355
X-RAY DIFFRACTIONf_angle_d1.0557270
X-RAY DIFFRACTIONf_dihedral_angle_d18.731969
X-RAY DIFFRACTIONf_chiral_restr0.062851
X-RAY DIFFRACTIONf_plane_restr0.005923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.31171310.26872455X-RAY DIFFRACTION87
2.4858-2.58530.28451270.25512546X-RAY DIFFRACTION90
2.5853-2.70290.31061300.24882581X-RAY DIFFRACTION91
2.7029-2.84540.29741380.23082589X-RAY DIFFRACTION92
2.8454-3.02360.26521440.22262669X-RAY DIFFRACTION94
3.0236-3.2570.2541430.20772724X-RAY DIFFRACTION96
3.257-3.58450.26141460.1862813X-RAY DIFFRACTION98
3.5845-4.10280.21251500.16982830X-RAY DIFFRACTION99
4.1028-5.16730.19861530.15732880X-RAY DIFFRACTION99
5.1673-39.96930.19781570.21062984X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44360.5717-0.00583.3581-0.55661.2132-0.05720.0909-0.0827-0.24560.0165-0.12030.14090.079300.51010.02060.00980.573-0.01570.48797.9185-16.392814.1721
21.79760.76830.02253.7029-0.24371.6887-0.02440.0758-0.0157-0.27770.0046-0.1338-0.0610.035400.5223-0.00880.01290.5720.00860.51131.167920.733814.4282
30000000000000000.63330.08940.04980.65830.03520.658216.6586-10.363417.2402
40.0097-0.0069-0.01150.00340.00610.00160.08630.11510.02490.12540.01040.19660.03160.1926-00.4937-0.1022-0.06680.50650.02210.532212.8922-6.074621.544
5-0.0153-0.0032-0.00380.01780.04280.0994-0.0464-0.0583-0.0512-0.02050.03120.0018-0.0222-0.0895-00.46290.08240.02240.45370.07370.457814.4242-18.119926.3725
6-0.0134-0.00050.0162-0.004-0.01460.0839-0.1355-0.215-0.036-0.0131-0.01420.0234-0.03710.02610.00010.47130.01490.05350.4981-0.04990.507624.774222.92826.5759
7-0.00110.00250.00170.00660.002-0.00110.0777-0.128-0.1110.0909-0.1472-0.0993-0.0788-0.10840.00010.5661-0.0391-0.03090.47530.02830.484325.883310.59422.4961
82.00011.99982.00022.000322.0002-0.4642-0.0018-0.72131.61390.0149-5.32942.448-0.20050.45140.90190.13060.02741.2090.08520.856221.210721.57172.1141
90000000000000-000.5419-0.1445-0.00410.5587-0.08340.584222.291915.007717.8493
102.0002222.00021.99972.0002-1.34-0.6875-2.76193.8081-0.0745-2.62112.52910.68951.42060.8475-0.1830.09341.29040.57290.521117.7568-17.88251.8565
112.00012.00011.99981.99971.99972.0001-1.44190.21661.45710.0738-0.0476-0.1669-1.53650.18661.47790.83870.0926-0.12710.96820.09420.774.2834.246522.2496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:364 )A16 - 364
2X-RAY DIFFRACTION2( CHAIN B AND RESID 16:364 )B16 - 364
3X-RAY DIFFRACTION3( CHAIN A AND RESID 369:369 )A369
4X-RAY DIFFRACTION4( CHAIN A AND RESID 370:370 )A370
5X-RAY DIFFRACTION5( CHAIN A AND RESID 371:371 )A371
6X-RAY DIFFRACTION6( CHAIN B AND RESID 372:372 )B372
7X-RAY DIFFRACTION7( CHAIN B AND RESID 371:371 )B371
8X-RAY DIFFRACTION8( CHAIN B AND RESID 369:369 )B369
9X-RAY DIFFRACTION9( CHAIN B AND RESID 370:370 )B370
10X-RAY DIFFRACTION10( CHAIN A AND RESID 372:372 )A372
11X-RAY DIFFRACTION11( CHAIN A AND RESID 374:374 )A374

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