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- PDB-5lqf: CDK1/CyclinB1/CKS2 in complex with NU6102 -

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Basic information

Entry
Database: PDB / ID: 5lqf
TitleCDK1/CyclinB1/CKS2 in complex with NU6102
Components
  • Cyclin-dependent kinase 1
  • Cyclin-dependent kinases regulatory subunit 2
  • G2/mitotic-specific cyclin-B1
KeywordsTRANSFERASE / CDK1 CYCLIN B CKS2 CELL CYCLE NU6102
Function / homology
Function and homology information


regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint ...regulation of Schwann cell differentiation / pronuclear fusion / cyclin B1-CDK1 complex / positive regulation of mitochondrial ATP synthesis coupled electron transport / Mitotic Prophase / positive regulation of mitotic sister chromatid segregation / histone kinase activity / Golgi disassembly / microtubule cytoskeleton organization involved in mitosis / G2/M DNA replication checkpoint / E2F-enabled inhibition of pre-replication complex formation / ventricular cardiac muscle cell development / Depolymerization of the Nuclear Lamina / positive regulation of attachment of spindle microtubules to kinetochore / MASTL Facilitates Mitotic Progression / regulation of mitotic cell cycle spindle assembly checkpoint / Activation of NIMA Kinases NEK9, NEK6, NEK7 / mitotic nuclear membrane disassembly / Phosphorylation of Emi1 / Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / patched binding / Nuclear Pore Complex (NPC) Disassembly / Transcriptional regulation by RUNX2 / Phosphorylation of the APC/C / outer kinetochore / meiosis I / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Initiation of Nuclear Envelope (NE) Reformation / protein localization to kinetochore / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / cyclin-dependent protein serine/threonine kinase activator activity / Condensation of Prometaphase Chromosomes / response to copper ion / chromosome condensation / centrosome cycle / [RNA-polymerase]-subunit kinase / cyclin-dependent protein serine/threonine kinase regulator activity / SCF ubiquitin ligase complex / mitotic metaphase chromosome alignment / G1/S-Specific Transcription / cyclin-dependent protein kinase activity / MAPK3 (ERK1) activation / response to amine / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / Regulation of APC/C activators between G1/S and early anaphase / regulation of embryonic development / cellular response to organic cyclic compound / response to axon injury / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / animal organ regeneration / Nuclear events stimulated by ALK signaling in cancer / cyclin-dependent protein serine/threonine kinase activity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to cadmium ion / Cyclin A/B1/B2 associated events during G2/M transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / positive regulation of cardiac muscle cell proliferation / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / epithelial cell differentiation / Hsp70 protein binding / APC/C:Cdc20 mediated degradation of Cyclin B / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / ERK1 and ERK2 cascade / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / RNA polymerase II CTD heptapeptide repeat kinase activity / cyclin binding / Condensation of Prophase Chromosomes / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / positive regulation of DNA replication / response to activity / ubiquitin binding / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / peptidyl-threonine phosphorylation / MAPK6/MAPK4 signaling / PKR-mediated signaling / spindle microtubule / regulation of circadian rhythm / mitotic spindle / response to toxic substance / spindle pole / microtubule cytoskeleton organization / cellular response to hydrogen peroxide / positive regulation of protein import into nucleus / positive regulation of protein localization to nucleus / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition
Similarity search - Function
: / Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : ...: / Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4SP / Cyclin-dependent kinase 1 / G2/mitotic-specific cyclin-B1 / Cyclin-dependent kinases regulatory subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCoxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B.J. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E. ...Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B.J. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Noble, M.E. / Newell, D.R. / Turner, D.M. / Sivaprakasam, M. / Wang, L.Z. / Wong, C. / Golding, B.T. / Griffin, R.J. / Endicott, J.A. / Cano, C.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Cyclin-Dependent Kinase (CDK) Inhibitors: Structure-Activity Relationships and Insights into the CDK-2 Selectivity of 6-Substituted 2-Arylaminopurines.
Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / ...Authors: Coxon, C.R. / Anscombe, E. / Harnor, S.J. / Martin, M.P. / Carbain, B. / Golding, B.T. / Hardcastle, I.R. / Harlow, L.K. / Korolchuk, S. / Matheson, C.J. / Newell, D.R. / Noble, M.E. / Sivaprakasam, M. / Tudhope, S.J. / Turner, D.M. / Wang, L.Z. / Wedge, S.R. / Wong, C. / Griffin, R.J. / Endicott, J.A. / Cano, C.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 1
B: G2/mitotic-specific cyclin-B1
C: Cyclin-dependent kinases regulatory subunit 2
D: Cyclin-dependent kinase 1
E: G2/mitotic-specific cyclin-B1
F: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2348
Polymers152,4296
Non-polymers8052
Water5,242291
1
A: Cyclin-dependent kinase 1
B: G2/mitotic-specific cyclin-B1
C: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6174
Polymers76,2143
Non-polymers4021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-20 kcal/mol
Surface area28660 Å2
MethodPISA
2
D: Cyclin-dependent kinase 1
E: G2/mitotic-specific cyclin-B1
F: Cyclin-dependent kinases regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6174
Polymers76,2143
Non-polymers4021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-22 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.040, 67.750, 85.060
Angle α, β, γ (deg.)103.88, 90.89, 90.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cyclin-dependent kinase 1 / CDK1 / Cell division control protein 2 homolog / Cell division protein kinase 1 / p34 protein kinase


Mass: 34553.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK1, CDC2, CDC28A, CDKN1, P34CDC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P06493, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase
#2: Protein G2/mitotic-specific cyclin-B1


Mass: 31369.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1, CCNB / Production host: Escherichia coli (E. coli) / References: UniProt: P14635
#3: Protein Cyclin-dependent kinases regulatory subunit 2 / CKS-2


Mass: 10290.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P33552
#4: Chemical ChemComp-4SP / O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE


Mass: 402.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H22N6O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.989 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 2.06→65.7 Å / Num. obs: 84841 / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.2
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 1.16 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YC3

4yc3


Resolution: 2.06→65.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 16.73 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25385 4136 4.9 %RANDOM
Rwork0.19764 ---
obs0.20037 80705 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.072 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0.34 Å2-3.14 Å2
2--2.62 Å2-0.1 Å2
3----1.6 Å2
Refinement stepCycle: 1 / Resolution: 2.06→65.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10174 0 56 291 10521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01910543
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210260
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.9714264
X-RAY DIFFRACTIONr_angle_other_deg1.2012.99423638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.72251252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25423.697476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.353151937
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0421565
X-RAY DIFFRACTIONr_chiral_restr0.1360.21558
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022411
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_it0.8381.1225011
X-RAY DIFFRACTIONr_mcbond_other0.8381.1225010
X-RAY DIFFRACTIONr_mcangle_it1.41.6756259
X-RAY DIFFRACTIONr_mcangle_other1.41.6756260
X-RAY DIFFRACTIONr_scbond_it0.9651.2535532
X-RAY DIFFRACTIONr_scbond_other0.9611.2535531
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4851.8418005
X-RAY DIFFRACTIONr_long_range_B_refined4.59313.4611978
X-RAY DIFFRACTIONr_long_range_B_other4.58613.32211940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 313 -
Rwork0.303 5925 -
obs--95.82 %
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)
11.4321-0.4877-0.15083.0917-0.69692.0724-0.00660.09740.083-0.00340.07810.0855-0.08150.1359-0.07150.1579-0.03310.28230.12-0.05150.525822.966-60.936182.405
22.7298-1.0389-0.28582.28940.05181.8656-0.02370.0631-0.05730.2053-0.02740.10640.02140.03870.05110.2628-0.06290.35030.0188-0.08830.48522.402-66.45211.177
33.98081.9707-0.80326.11372.00967.39080.064-0.01650.1096-0.06980.1854-0.4049-0.16120.6647-0.24940.2920.01620.34180.2742-0.02970.470430.808-30.053179.633
41.38130.3067-0.48213.54840.38752.0103-0.0937-0.0580.04410.13470.160.0481-0.0141-0.1053-0.06620.20210.050.29650.16640.0010.4953-15.959-94.727236.608
52.68221.0806-0.37042.3391-0.36132.196-0.1121-0.0322-0.0322-0.16740.0296-0.06510.0137-0.02950.08250.25090.0090.33160.00280.01180.45444.688-100.328207.842
64.5813-1.669-1.26147.9544-3.06547.42730.08910.22220.180.39610.73261.0205-0.5097-1.198-0.82170.42030.14110.45330.4110.13020.6207-24.553-64.189239.146
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 289
2X-RAY DIFFRACTION2B166 - 429
3X-RAY DIFFRACTION3C1 - 74
4X-RAY DIFFRACTION4D-2 - 289
5X-RAY DIFFRACTION5E166 - 429
6X-RAY DIFFRACTION6F1 - 74

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