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- PDB-2bzk: CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND PIMTIDE -

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Basic information

Entry
Database: PDB / ID: 2bzk
TitleCRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH AMPPNP AND PIMTIDE
Components
  • PIMTIDE
  • PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / COMPLEX TRANSFERASE-PEPTIDE / PIM1 / KINASE / CANCER / LEUKEMIA / ATP-BINDING / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION / PROTO- ONCOGENE / SERINE/THREONINE-PROTEIN KINASE / TRANSFERASE
Function / homology
Function and homology information


positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase 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 cardiac muscle cell proliferation ...positive regulation of cardioblast proliferation / positive regulation of cyclin-dependent protein serine/threonine kinase 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 cardiac muscle cell proliferation / positive regulation of brown fat cell differentiation / Signaling by FLT3 fusion proteins / positive regulation of TORC1 signaling / regulation of transmembrane transporter activity / negative regulation of innate immune response / regulation of mitotic cell cycle / protein serine/threonine kinase activator activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / protein autophosphorylation / Interleukin-4 and Interleukin-13 signaling / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / 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 / cytosol / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase pim-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDebreczeni, J.E. / Bullock, A. / Knapp, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
CitationJournal: To be Published
Title: Crystal Structure of the Human Pim1 in Complex with Amppnp and Pimtide
Authors: Debreczeni, J.E. / Bullock, A. / Knapp, S. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
History
DepositionAug 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PIMTIDE
B: PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7303
Polymers37,2232
Non-polymers5061
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)97.889, 97.889, 80.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsTHE PROTEIN (CHAIN B) IN THIS ENTRY IS IN COMPLEX WITHA PEPTIDE (CHAIN A) AND IS HENCE ANNOTATED AS DIMERIC.FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 THEMEAN DIFFERENCE IN ACCESSIBLE SURFACE AREA PER

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Components

#1: Protein/peptide PIMTIDE


Mass: 1590.858 Da / Num. of mol.: 1 / Fragment: PIM1 CONSENSUS PEPTIDE, RESIDUES 3-9 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#2: Protein PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1


Mass: 35632.602 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOFORM MUTATION R250G / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P11-TORONTO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11309, EC: 2.7.1.37
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPOSSIBLE ROLE IN SIGNAL TRANSDUCTION IN BLOOD CELLS ENGINEERED RESIDUE IN CHAIN B, ARG 250 TO GLY
Has protein modificationN
Sequence detailsISOFORM MUTATION R250G

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.1 M SUCCINATE PHOSPHATE GLYCINE BUFFER PH 6, 30% PEG1K, 0.5% DMSO, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 20, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 16216 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 7.33 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.43
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 6.24 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.28 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWS

1xws


Resolution: 2.45→42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 14.539 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 814 5 %RANDOM
Rwork0.189 ---
obs0.191 15369 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å21.21 Å20 Å2
2--2.43 Å20 Å2
3----3.64 Å2
Refinement stepCycle: LAST / Resolution: 2.45→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 31 23 2277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212315
X-RAY DIFFRACTIONr_bond_other_d0.0010.022086
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9633150
X-RAY DIFFRACTIONr_angle_other_deg0.79234814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33422.783115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2381522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
X-RAY DIFFRACTIONr_nbd_refined0.2070.2433
X-RAY DIFFRACTIONr_nbd_other0.1780.22081
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21124
X-RAY DIFFRACTIONr_nbtor_other0.0840.21399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.51393
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05622217
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63631040
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7444.5933
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 62
Rwork0.33 1120
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)
17.1183-0.41070.5715.1394-1.74754.4532-0.1314-0.72760.0699-0.04880.12810.311-0.2299-0.55520.0033-0.2050.08930.067-0.05460.0227-0.220916.79834.268.557
22.1740.2673-0.23732.1376-0.09493.2518-0.01220.0195-0.0179-0.07960.18520.06990.0966-0.1109-0.1729-0.16010.0211-0.0395-0.21630.0556-0.150537.43424.705-2.795
33.67780.898-11.17512.9599-8.250136.3481-0.14941.4185-0.6005-0.56460.69860.14160.7207-2.6283-0.5491-0.22990.054-0.1918-0.03240.185-0.005326.23125.695-13.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B33 - 123
2X-RAY DIFFRACTION2B124 - 305
3X-RAY DIFFRACTION3A3 - 9

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