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- PDB-4eny: Crystal Structure of Pim-1 kinase in complex with (2E,5Z)-2-(2-ch... -

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Basic information

Entry
Database: PDB / ID: 4eny
TitleCrystal Structure of Pim-1 kinase in complex with (2E,5Z)-2-(2-chlorophenylimino)-5-(4-hydroxy-3-methoxybenzylidene)thiazolidin-4-one
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/INHIBITOR / Pim-1 kinase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / positive regulation of cyclin-dependent protein serine/threonine kinase activity / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / positive regulation of cyclin-dependent protein serine/threonine kinase activity / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / nucleolus / apoptotic process / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain ...Serine/threonine-protein kinase pim-1/2/3 / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase 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-J19 / PHOSPHATE ION / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsParker, L.J. / Handa, N. / Yokoyama, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Flexibility of the P-loop of Pim-1 kinase: observation of a novel conformation induced by interaction with an inhibitor
Authors: Parker, L.J. / Watanabe, H. / Tsuganezawa, K. / Tomabechi, Y. / Handa, N. / Shirouzu, M. / Yuki, H. / Honma, T. / Ogawa, N. / Nagano, T. / Yokoyama, S. / Tanaka, A.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Serine/threonine-protein kinase pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8145
Polymers34,1881
Non-polymers6264
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.765, 96.765, 80.963
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase pim-1


Mass: 34187.727 Da / Num. of mol.: 1 / Fragment: Protein kinase domain, UNP RESIDUES 120-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pCR2.1-TOPO / Production host: cell-free protein synthesis (unknown)
References: UniProt: P11309, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 64 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-J19 / (2Z,5Z)-2-[(2-chlorophenyl)imino]-5-(4-hydroxy-3-methoxybenzylidene)-1,3-thiazolidin-4-one


Mass: 360.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13ClN2O3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Citrate buffer, pH 5.5, 200mM NaCl, 1M NH4HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.801→37.216 Å / Num. all: 10721 / Num. obs: 10721 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 64.3 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 29.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.8-2.9512.50.420.4031.91942215550.1180.420.4036.8100
2.95-3.1312.50.3010.2892.41846614730.0850.3010.2899.7100
3.13-3.3512.60.1860.1784.31741613850.0520.1860.17815.6100
3.35-3.6112.60.110.1067.21625112890.0310.110.10624.7100
3.61-3.9612.60.0720.06910.91493111830.020.0720.06934.1100
3.96-4.4312.60.0480.04616.31363510800.0130.0480.04643.3100
4.43-5.1112.70.0410.03917.8121119570.0120.0410.03949.5100
5.11-6.2612.70.0460.04417.1102628110.0130.0460.04447.7100
6.26-8.8512.50.0340.03322.279106330.010.0340.03360.5100
8.85-37.21611.60.0230.02227.141213550.0070.0230.02276.898.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å37.21 Å
Translation2.8 Å37.21 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER2.3.0phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UMX

3umx


Resolution: 2.801→31.674 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8526 / SU ML: 0.47 / σ(F): 1.37 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 541 5.06 %RANDOM
Rwork0.1726 ---
obs0.1751 10689 99.98 %-
all-10693 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.924 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 153.38 Å2 / Biso mean: 44.7889 Å2 / Biso min: 0.24 Å2
Baniso -1Baniso -2Baniso -3
1-2.325 Å20 Å20 Å2
2--2.325 Å20 Å2
3----4.6499 Å2
Refinement stepCycle: LAST / Resolution: 2.801→31.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2140 0 39 60 2239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052242
X-RAY DIFFRACTIONf_angle_d0.7773037
X-RAY DIFFRACTIONf_chiral_restr0.059321
X-RAY DIFFRACTIONf_plane_restr0.004389
X-RAY DIFFRACTIONf_dihedral_angle_d13.792823
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.8015-3.08320.37821430.2675251226552512
3.0832-3.52890.2391370.1687251726542517
3.5289-4.4440.19881310.1487253226632532
4.444-31.67580.18051300.1625258727172587
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)
12.55281.03871.05653.5979-0.35853.2094-0.0014-0.1899-0.13780.1966-0.16780.00590.34-0.06660.09910.1227-0.1610.04340.24730.05770.0409-69.2835114.17826.8365
23.23341.5916-1.82734.206-1.72213.65780.03270.17320.11190.0816-0.01580.23290.0882-0.5484-0.04570.142-0.0174-0.07070.2566-0.01130.1739-66.8887122.65573.1116
32.6043-0.63220.44931.551-0.48982.40430.0588-0.1278-0.028-0.10210.0261-0.05880.31490.0139-0.06630.0973-0.0238-0.03760.10660.00470.0977-50.7957123.5501-0.1596
43.7273-0.49990.3093.7781-0.55854.89050.1029-0.2220.30270.1216-0.0251-0.5391-0.33610.5193-0.07530.0788-0.02770.03290.168-0.02640.2093-42.5148133.4007-4.3928
51.674-1.16360.87297.67131.37055.1202-0.0294-0.15250.3595-0.099-0.11560.2604-0.3555-0.56310.22910.11490.12110.08060.10780.04420.2747-61.9586143.4078-0.7374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 37:95)A37 - 95
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 96:140)A96 - 140
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 141:250)A141 - 250
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 251:290)A251 - 290
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 291:305)A291 - 305

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