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- PDB-5n4n: Crystal structure of human Pim-1 kinase in complex with a consens... -

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Basic information

Entry
Database: PDB / ID: 5n4n
TitleCrystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment like molecule 3,4-dimethyl-5-(1H-1,2,4-triazol-3-yl)thiophene-2-carbonitrile
Components
  • Pimtide
  • Serine/threonine-protein kinase pim-1
KeywordsTRANSFERASE / Serine Threonine Kinase / proto-oncogene / Fragment / PIM-1 / Consensus peptide
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of transmembrane transporter activity / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / cellular detoxification / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / positive regulation of cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of mitotic cell cycle / negative regulation of innate immune response / protein serine/threonine kinase activator activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleolus / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase pim-1/2/3 / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-8M8 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSiefker, C. / Heine, A. / Klebe, G.
CitationJournal: to be published
Title: A crystallographic fragment study with human Pim-1 kinase
Authors: Siefker, C. / Heine, A. / Hardes, K. / Steinmetzer, A. / Klebe, G.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Aug 14, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3Jan 17, 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

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Assembly

Deposited unit
A: Serine/threonine-protein kinase pim-1
B: Pimtide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4303
Polymers37,2252
Non-polymers2041
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint3 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.517, 98.517, 80.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 35632.602 Da / Num. of mol.: 1 / Mutation: R250G
Source method: isolated from a genetically manipulated source
Details: Isofrom 2 of PIM-1 kinase / Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pLIC-SGC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Protein/peptide Pimtide


Mass: 1592.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PIM-1 consensus peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-8M8 / 3,4-dimethyl-5-(1~{H}-1,2,4-triazol-3-yl)thiophene-2-carbonitrile


Mass: 204.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: HEPES NaCl Glycerol DTT BIS-TRIS-propane PEG3350 Ethylene-glycol DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2016 / Details: Silicon
RadiationMonochromator: Si-111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 26155 / % possible obs: 99.8 % / Redundancy: 8.49 % / CC1/2: 0.99 / Rrim(I) all: 0.053 / Net I/σ(I): 27.46
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 8.52 % / Mean I/σ(I) obs: 6.88 / Num. unique obs: 4178 / CC1/2: 0.94 / Rrim(I) all: 0.537 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WE8

3we8


Resolution: 2.09→49.258 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.1879 1308 5 %
Rwork0.1591 --
obs0.1605 26155 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→49.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 14 115 2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072341
X-RAY DIFFRACTIONf_angle_d0.7953178
X-RAY DIFFRACTIONf_dihedral_angle_d20.5111385
X-RAY DIFFRACTIONf_chiral_restr0.054335
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.093-2.17680.21521420.17882704X-RAY DIFFRACTION99
2.1768-2.27590.22191450.16922757X-RAY DIFFRACTION100
2.2759-2.39590.2191460.1612767X-RAY DIFFRACTION100
2.3959-2.5460.20591450.16512756X-RAY DIFFRACTION100
2.546-2.74260.2111440.17372731X-RAY DIFFRACTION100
2.7426-3.01850.22831450.17152759X-RAY DIFFRACTION100
3.0185-3.45520.18951450.16532765X-RAY DIFFRACTION100
3.4552-4.35280.16281470.14792783X-RAY DIFFRACTION100
4.3528-49.27210.17141490.15212825X-RAY DIFFRACTION100
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)
15.69141.3367-0.53384.5652-1.02924.1525-0.131-0.1053-0.5644-0.25310.0650.3410.4794-0.19480.02680.4250.0343-0.03740.3053-0.04230.315786.121682.44-11.8717
21.14580.07250.09262.06820.08932.3640.1019-0.02070.00420.0459-0.03960.04420.03120.0438-0.06680.24590.0130.02080.29140.01260.24389.5541103.0137-3.268
38.6581-1.24265.25353.6097-0.0816.83690.4572-0.7936-0.49940.0122-0.01990.58160.2105-0.6337-0.36570.454-0.0766-0.00290.36150.12250.420983.744495.51758.0432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 305 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 10 )

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