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- PDB-4ll5: Crystal Structure of Pim-1 in complex with the fluorescent compou... -

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Basic information

Entry
Database: PDB / ID: 4ll5
TitleCrystal Structure of Pim-1 in complex with the fluorescent compound SKF86002
ComponentsSerine/threonine-protein kinase pim-1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / co-crystallization / SKF86002 / fluorescence / inhibitor screening / kinase / TRANSFERASE-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 / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / ribosomal small subunit binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response ...positive regulation of cardioblast proliferation / 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 cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / 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 / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase pim-1/2/3 / : / 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 ...Serine/threonine-protein kinase pim-1/2/3 / : / 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-SK8 / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsParker, L.J. / Tanaka, A. / Handa, N. / Honda, K. / Tomabechi, Y. / Shirouzu, M. / Yokoyama, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002.
Authors: Parker, L.J. / Taruya, S. / Tsuganezawa, K. / Ogawa, N. / Mikuni, J. / Honda, K. / Tomabechi, Y. / Handa, N. / Shirouzu, M. / Yokoyama, S. / Tanaka, A.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
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 / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,8947
Polymers34,1881
Non-polymers7066
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.650, 98.650, 80.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Serine/threonine-protein kinase pim-1 / PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1


Mass: 34187.727 Da / Num. of mol.: 1 / Fragment: Protein Kinase domain, UNP resodies 120-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: P11309, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SK8 / 6-(4-fluorophenyl)-5-(pyridin-4-yl)-2,3-dihydroimidazo[2,1-b][1,3]thiazole / SKF-86002


Mass: 297.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12FN3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.3 Å3/Da / Density % sol: 62.7 % / Mosaicity: 0.13 °
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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→85.433 Å / Num. obs: 29928 / % possible obs: 99.4 % / Redundancy: 11.2 % / Biso Wilson estimate: 26.29 Å2 / Rsym value: 0.115 / Net I/σ(I): 15.6
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
2-2.1111.30.4190.41.94909443340.1240.4190.46.498.9
2.11-2.2411.30.2950.2812.74666841250.0870.2950.2818.899.1
2.24-2.3911.30.2050.1953.84333738460.0610.2050.19512.399.3
2.39-2.5811.20.1670.1594.54047136000.050.1670.15914.899.3
2.58-2.8311.20.1330.1275.33721733250.040.1330.12717.499.6
2.83-3.1611.10.1130.1075.83347030080.0340.1130.10720.199.6
3.16-3.65110.1030.0985.82954626820.0310.1030.09822.699.8
3.65-4.4710.40.0980.0936.12352622540.030.0980.09323.2100
4.47-6.3211.10.0990.0945.91956617630.030.0990.09424.9100
6.32-42.71711.10.1010.0965.2110029910.030.1010.09625.999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.55 Å58.6 Å
Translation2.55 Å58.6 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.1phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UIX

3uix


Resolution: 2→42.717 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8914 / SU ML: 0.13 / σ(F): 1.36 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 1521 5.08 %
Rwork0.1682 --
obs0.1693 29915 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.64 Å2 / Biso mean: 37.1657 Å2 / Biso min: 14.04 Å2
Refinement stepCycle: LAST / Resolution: 2→42.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 46 173 2399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032295
X-RAY DIFFRACTIONf_angle_d0.7023109
X-RAY DIFFRACTIONf_chiral_restr0.051326
X-RAY DIFFRACTIONf_plane_restr0.003401
X-RAY DIFFRACTIONf_dihedral_angle_d14.286846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.06470.24561280.19062592272099
2.0647-2.13850.21951440.1842546269099
2.1385-2.22420.21511380.182559269799
2.2242-2.32540.21591450.17362550269599
2.3254-2.4480.19781420.17962573271599
2.448-2.60130.23191230.17272586270999
2.6013-2.80210.18871230.176725822705100
2.8021-3.0840.16781560.174925732729100
3.084-3.53010.17931400.164525882728100
3.5301-4.44690.17241360.141825982734100
4.4469-42.72640.18161460.17326472793100
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)
14.1602-0.5588-1.20856.69054.83768.0024-0.07890.2419-0.5707-0.07470.14970.26490.3834-0.36250.00790.2885-0.1327-0.00860.39420.04590.39364.2575-126.8708-2.0778
24.7836-0.0661-1.38394.73320.39986.0469-0.0110.5590.74560.40340.0390.2993-0.8888-0.5818-0.02730.2779-0.0107-0.02890.36440.12440.367863.2797-113.1452-5.8656
35.3897-0.06832.54960.79230.03792.9196-0.01470.3629-0.26960.01980.12280.18350.1043-0.0983-0.13350.2325-0.07390.02420.23870.01550.22473.9211-119.7216-2.3802
42.1674-0.85910.6162.9012-0.97782.4358-0.07270.11660-0.0910.1930.14960.036-0.2113-0.13450.1714-0.05770.02650.19190.00990.148882.7924-112.5288-1.4905
52.839-1.65842.17474.2395-1.58894.3314-0.1602-0.1250.11670.32790.15860.1659-0.3927-0.2179-0.00830.2048-0.01070.05460.1835-0.00510.189684.2332-101.1778.2445
62.6795-1.02870.77614.0871-0.08455.8195-0.03070.14050.16060.0890.0467-0.2852-0.25630.2132-0.00680.1429-0.06580.00940.1549-0.01010.17496.1784-105.39256.7936
76.98462.7536-1.42422.0315-2.56247.6441-0.0260.5183-0.94280.04410.2764-0.65650.83720.0868-0.11750.37820.0764-0.0280.2182-0.06280.391194.7434-127.33382.8118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 34:61 )A34 - 61
2X-RAY DIFFRACTION2chain 'A' and (resseq 62:87 )A62 - 87
3X-RAY DIFFRACTION3chain 'A' and (resseq 88:140 )A88 - 140
4X-RAY DIFFRACTION4chain 'A' and (resseq 141:204 )A141 - 204
5X-RAY DIFFRACTION5chain 'A' and (resseq 205:250 )A205 - 250
6X-RAY DIFFRACTION6chain 'A' and (resseq 251:290 )A251 - 290
7X-RAY DIFFRACTION7chain 'A' and (resseq 291:305 )A291 - 305

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