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- PDB-2vwi: Structure of the OSR1 kinase, a hypertension drug target -

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Basic information

Entry
Database: PDB / ID: 2vwi
TitleStructure of the OSR1 kinase, a hypertension drug target
ComponentsSERINE/THREONINE-PROTEIN KINASE OSR1
KeywordsTRANSFERASE / KINASE / STE KINASE / HYPERTENSION
Function / homology
Function and homology information


chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / osmosensory signaling pathway / cellular hyperosmotic response / cell volume homeostasis ...chemokine (C-C motif) ligand 21 signaling pathway / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of potassium ion transmembrane transport / renal sodium ion absorption / positive regulation of T cell chemotaxis / cellular hypotonic response / cellular response to chemokine / osmosensory signaling pathway / cellular hyperosmotic response / cell volume homeostasis / peptidyl-threonine phosphorylation / protein autophosphorylation / response to oxidative stress / 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 / intracellular signal transduction / protein phosphorylation / response to xenobiotic stimulus / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 OSR1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.15 Å
AuthorsVilla, F. / Deak, M. / Alessi, D.R. / vanAalten, D.M.F.
CitationJournal: Proteins / Year: 2008
Title: Structure of the Osr1 Kinase, a Hypertension Drug Target.
Authors: Villa, F. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionJun 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 17, 2013Group: Database references / Derived calculations
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE OSR1
B: SERINE/THREONINE-PROTEIN KINASE OSR1
C: SERINE/THREONINE-PROTEIN KINASE OSR1
D: SERINE/THREONINE-PROTEIN KINASE OSR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,25422
Polymers135,9894
Non-polymers4,26418
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-24.3 kcal/mol
Surface area65700 Å2
MethodPQS
Unit cell
Length a, b, c (Å)74.130, 99.900, 158.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SERINE/THREONINE-PROTEIN KINASE OSR1 / OXIDATIVE STRESS- RESPONSIVE 1 PROTEIN / OSR1


Mass: 33997.336 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, RESIDUES 1-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: O95747, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Au
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.46 Å3/Da / Density % sol: 49.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 65284 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 48.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.8 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIR
Starting model: NONE

Resolution: 2.15→19.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / SU B: 12.626 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 637 1 %RANDOM
Rwork0.253 ---
obs0.253 63160 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8137 0 138 228 8503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.98811418
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.39751040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04724.683331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.445151485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3871531
X-RAY DIFFRACTIONr_chiral_restr0.0640.21293
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026129
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.23796
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.25767
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2173
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2421.55407
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42928364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.47633509
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8454.53053
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: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.373 39
Rwork0.303 4041
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)
11.2885-0.06380.42781.04820.01873.8983-0.10390.31240.3404-0.08010.05250.0098-0.2806-0.00350.0513-0.2399-0.01710.0014-0.17490.1013-0.22494.3789147.921-21.2166
21.46120.2630.29671.91740.78352.68430.0932-0.09590.18760.3187-0.065-0.2943-0.02940.0356-0.0283-0.3315-0.046-0.0664-0.24640.0381-0.176152.0637152.201-34.0234
31.2436-0.4319-0.46021.64921.59622.8658-0.0626-0.07250.185-0.1369-0.06960.071-0.0393-0.17960.1321-0.298-0.0183-0.0158-0.2556-0.0433-0.22666.5002147.22115.8987
41.0177-0.6338-0.63991.58040.79052.247-0.01420.0568-0.1629-0.0137-0.0935-0.0176-0.0079-0.03290.1077-0.3045-0.05060.0058-0.2421-0.071-0.236765.64898.7854-18.918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 291
2X-RAY DIFFRACTION2B9 - 291
3X-RAY DIFFRACTION3C9 - 291
4X-RAY DIFFRACTION4D8 - 291

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