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- PDB-5htc: Crystal structure of haspin (GSG2) in complex with bisubstrate in... -

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Basic information

Entry
Database: PDB / ID: 5htc
TitleCrystal structure of haspin (GSG2) in complex with bisubstrate inhibitor ARC-3372
Components
  • ARC-3372 INHIBITOR
  • Serine/threonine-protein kinase haspin
KeywordsTRANSFERASE / KINASE / INHIBITOR / ALLOSTERIC / STRUCTURAL GENOMICS CONSORTIUM (SGC) / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / bisubstrate inhibitor
Function / homology
Function and homology information


histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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-66M / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChaikuad, A. / Heroven, C. / Lavogina, D. / Kestav, K. / Uri, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Co-crystal structures of the protein kinase haspin with bisubstrate inhibitors.
Authors: Lavogina, D. / Kestav, K. / Chaikuad, A. / Heroven, C. / Knapp, S. / Uri, A.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase haspin
C: ARC-3372 INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3627
Polymers41,5152
Non-polymers8475
Water7,278404
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-23 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.970, 78.903, 81.060
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 / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Serine/threonine-protein kinase haspin / Germ cell-specific gene 2 protein / H-haspin / Haploid germ cell-specific nuclear protein kinase


Mass: 40711.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: kinase domain (465-798) / Source: (gene. exp.) Homo sapiens (human) / Gene: GSG2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Protein/peptide ARC-3372 INHIBITOR


Mass: 803.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 409 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-66M / (2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name)


Mass: 509.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N7O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 52-60% MPD and 0.1 M SPG pH 6.5-7.0 / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 1.5→25.02 Å / Num. obs: 79693 / % possible obs: 99 % / Redundancy: 5.6 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 5.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QTC

4qtc


Resolution: 1.5→25.02 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.773 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17125 3678 4.6 %RANDOM
Rwork0.14962 ---
obs0.15062 75949 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0 Å20 Å2
2--0.42 Å2-0 Å2
3---0.23 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.5→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 56 404 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193020
X-RAY DIFFRACTIONr_bond_other_d0.0030.0192908
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9514108
X-RAY DIFFRACTIONr_angle_other_deg0.89636736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91824.733131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66715525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8731512
X-RAY DIFFRACTIONr_chiral_restr0.1060.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02692
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_it0.7761.0221360
X-RAY DIFFRACTIONr_mcbond_other0.7641.021359
X-RAY DIFFRACTIONr_mcangle_it1.2271.5311709
X-RAY DIFFRACTIONr_mcangle_other1.2271.5311710
X-RAY DIFFRACTIONr_scbond_it1.5161.3881660
X-RAY DIFFRACTIONr_scbond_other1.5161.3921661
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4382.0012382
X-RAY DIFFRACTIONr_long_range_B_refined7.01710.893664
X-RAY DIFFRACTIONr_long_range_B_other7.01610.9033665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 276 -
Rwork0.176 5400 -
obs--96.55 %
Refinement TLS params.Method: refined / Origin x: 25.9649 Å / Origin y: 25.5653 Å / Origin z: 8.3277 Å
111213212223313233
T0.0108 Å20.0101 Å20.0035 Å2-0.0134 Å20.0031 Å2--0.0076 Å2
L1.2354 °20.54 °20.3448 °2-1.5428 °20.4452 °2--0.9946 °2
S0.0402 Å °-0.0028 Å °0.0479 Å °-0.011 Å °0.0177 Å °0.0013 Å °-0.0237 Å °-0.05 Å °-0.0579 Å °

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