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- PDB-3oht: Crystal Structure of Salmo Salar p38alpha -

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Basic information

Entry
Database: PDB / ID: 3oht
TitleCrystal Structure of Salmo Salar p38alpha
Componentsp38a
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase Serine/threonine-protein kinase Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


MAP kinase activity / mitogen-activated protein kinase / ATP binding
Similarity search - Function
Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-1N1 / Mitogen-activated protein kinase
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRothweiler, U. / Johnson, K. / Engh, R.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: p38alpha MAP kinase dimers with swapped activation segments and a novel catalytic loop conformation
Authors: Rothweiler, U. / Aberg, E. / Johnson, K.A. / Hansen, T.E. / Jorgensen, J.B. / Engh, R.A.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Database references / Structure summary
Revision 1.3Sep 6, 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 / 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_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: p38a
B: p38a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0608
Polymers89,9162
Non-polymers2,1446
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9990 Å2
ΔGint-83 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.780, 100.930, 67.890
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

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Components

#1: Protein p38a


Mass: 44957.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: p38a / Production host: Escherichia coli (E. coli) / References: UniProt: A9UJZ9
#2: Chemical
ChemComp-1N1 / N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE / Dasatinib


Mass: 488.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H26ClN7O2S / Comment: medication*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.01 M MgCl2, 0.05 M Tris/HCl, 1.6 M NH4SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 22427 / Num. obs: 22427 / % possible obs: 90 % / Redundancy: 2.4 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.08
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 2.36 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.65 / Num. unique all: 1653 / % possible all: 90.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREP10.2.23phasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W82

1w82


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.855 / SU B: 14.494 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1147 5.1 %RANDOM
Rwork0.232 ---
all0.235 22427 --
obs0.235 21280 90.01 %-
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: 39.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.01 Å2
2--0.33 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 142 107 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9927678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7715658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6324.06266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72315970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.881536
X-RAY DIFFRACTIONr_chiral_restr0.080.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214308
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4381.53318
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82425404
X-RAY DIFFRACTIONr_scbond_it0.95432338
X-RAY DIFFRACTIONr_scangle_it1.6964.52274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1324MEDIUM POSITIONAL0.10.5
1364LOOSE POSITIONAL0.225
1324MEDIUM THERMAL0.152
1364LOOSE THERMAL0.2310
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 82 -
Rwork0.263 1568 -
obs--90.96 %

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