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- PDB-1yxu: Crystal Structure of Kinase Pim1 in Complex with AMP -

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Basic information

Entry
Database: PDB / ID: 1yxu
TitleCrystal Structure of Kinase Pim1 in Complex with AMP
ComponentsProto-oncogene serine/threonine-protein kinase Pim-1
KeywordsTRANSFERASE / Ser/Thr protein kinase
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / 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 / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of 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 / Protein kinase, ATP binding site ...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
ADENOSINE MONOPHOSPHATE / IMIDAZOLE / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Proto-oncogene Kinase Pim1: A Target of Aberrant Somatic Hypermutations in Diffuse Large Cell Lymphoma.
Authors: Kumar, A. / Mandiyan, V. / Suzuki, Y. / Zhang, C. / Rice, J. / Tsai, J. / Artis, D.R. / Ibrahim, P. / Bremer, R.
History
DepositionFeb 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Proto-oncogene serine/threonine-protein kinase Pim-1
B: Proto-oncogene serine/threonine-protein kinase Pim-1
C: Proto-oncogene serine/threonine-protein kinase Pim-1
D: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,99512
Polymers135,3294
Non-polymers1,6658
Water6,918384
1
A: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2493
Polymers33,8321
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2493
Polymers33,8321
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2493
Polymers33,8321
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Proto-oncogene serine/threonine-protein kinase Pim-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2493
Polymers33,8321
Non-polymers4162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.745, 195.745, 80.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 35 - 304 / Label seq-ID: 7 - 276

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Proto-oncogene serine/threonine-protein kinase Pim-1


Mass: 33832.320 Da / Num. of mol.: 4 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11309, EC: 2.7.1.37
#2: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.8 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→72.55 Å / Num. all: 84753 / Num. obs: 84733 / % possible obs: 97.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 2.24→2.36 Å / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.1.25refinement
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→72.55 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.852 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.5 / ESU R: 0.252 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4111 5 %RANDOM
Rwork0.228 ---
all0.231 84753 --
obs0.228 78366 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.785 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å21.11 Å20 Å2
2--2.22 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.24→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8889 0 112 384 9385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0219252
X-RAY DIFFRACTIONr_bond_other_d0.0030.028312
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.95712565
X-RAY DIFFRACTIONr_angle_other_deg0.98319252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.09351087
X-RAY DIFFRACTIONr_chiral_restr0.1040.21339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210253
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022007
X-RAY DIFFRACTIONr_nbd_refined0.2050.22010
X-RAY DIFFRACTIONr_nbd_other0.2330.29887
X-RAY DIFFRACTIONr_nbtor_other0.0840.25607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2369
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_mcbond_it0.4841.55434
X-RAY DIFFRACTIONr_mcangle_it0.87528806
X-RAY DIFFRACTIONr_scbond_it1.37533818
X-RAY DIFFRACTIONr_scangle_it2.2334.53759
Refine LS restraints NCS

Ens-ID: 1 / Number: 4242 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.395
2Bloose positional0.415
3Cloose positional0.345
4Dloose positional0.395
1Aloose thermal1.8710
2Bloose thermal1.1810
3Cloose thermal1.0210
4Dloose thermal1.4910
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.336 304
Rwork0.3 5750
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)
12.4355-0.21110.60322.5146-0.44834.47010.1173-0.0281-0.41680.09640.0387-0.04110.96350.2952-0.1560.18620.0601-0.04260.0262-0.04350.141710.09698.09525.692
23.0401-0.49881.15233.5935-1.01073.30140.0878-0.022-0.23410.17370.12720.0865-0.13730.4305-0.2150.2108-0.02020.16610.1083-0.04840.249518.83657.22912.905
34.030.3487-1.17412.5224-0.48052.75210.1591-0.1570.14890.04720.06930.13760.2799-0.2444-0.22850.0988-0.03650.00440.12980.00330.2854-7.53640.59239.677
42.27930.43340.24364.53980.85221.46550.0473-0.0129-0.15090.28790.0338-0.2334-0.2772-0.0713-0.08110.3186-0.0340.11920.06140.07630.2246-8.73671.77466.523
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA33 - 3055 - 277
22BB33 - 3055 - 277
33CC34 - 3056 - 277
44DD33 - 3055 - 277

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