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- PDB-4w9x: Crystal Structure of BMP-2-inducible kinase in complex with baric... -

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Basic information

Entry
Database: PDB / ID: 4w9x
TitleCrystal Structure of BMP-2-inducible kinase in complex with baricitinib
ComponentsBMP-2-inducible protein kinase
KeywordsTRANSFERASE / kinase / small-molecule / catalytic domain / protein binding / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / : / 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 domain profile. ...BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / : / 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baricitinib / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsSorrell, F.J. / Elkins, J.M. / Krojer, T. / Williams, E. / Savitsky, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2016
Title: Family-wide Structural Analysis of Human Numb-Associated Protein Kinases.
Authors: Sorrell, F.J. / Szklarz, M. / Abdul Azeez, K.R. / Elkins, J.M. / Knapp, S.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2874
Polymers34,7911
Non-polymers4963
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint7 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 111.410, 163.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein BMP-2-inducible protein kinase / BIKe


Mass: 34791.035 Da / Num. of mol.: 1 / Fragment: UNP residues 38-345 / Mutation: K320A, K321A
Source method: isolated from a genetically manipulated source
Details: Kinase domain with two surface entropy mutations (K320A, K321A)
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2K, BIKE, HRIHFB2017 / Plasmid: pNIC-ZB / Production host: Escherichia coli Bl21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: Q9NSY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-3JW / Baricitinib


Mass: 371.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N7O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 4M sodium chloride, 0.1M bis-Tris pH 5.5, freshly purified protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.14→33 Å / Num. obs: 21713 / % possible obs: 99.3 % / Redundancy: 2.6 % / Net I/σ(I): 9.6
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→92.12 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.099 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22949 1078 5 %RANDOM
Rwork0.18718 ---
obs0.18932 20634 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-0 Å2
2--0.85 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 2.14→92.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 34 129 2442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192361
X-RAY DIFFRACTIONr_bond_other_d0.0010.022201
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9713211
X-RAY DIFFRACTIONr_angle_other_deg0.8183.0045041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4315297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52624.44499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4891511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
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_it1.8022.7421197
X-RAY DIFFRACTIONr_mcbond_other1.8012.741196
X-RAY DIFFRACTIONr_mcangle_it2.8974.0931491
X-RAY DIFFRACTIONr_mcangle_other2.8964.0951492
X-RAY DIFFRACTIONr_scbond_it2.1652.9061164
X-RAY DIFFRACTIONr_scbond_other2.1642.9051165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4864.2711719
X-RAY DIFFRACTIONr_long_range_B_refined5.67422.1562670
X-RAY DIFFRACTIONr_long_range_B_other5.60221.9182634
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 80 -
Rwork0.268 1488 -
obs--99.3 %
Refinement TLS params.Method: refined / Origin x: 0.8502 Å / Origin y: -28.2771 Å / Origin z: -24.5918 Å
111213212223313233
T0.2234 Å2-0.016 Å2-0.0006 Å2-0.0314 Å20.0111 Å2--0.0078 Å2
L0.2853 °20.2508 °2-0.3015 °2-0.8433 °2-0.8037 °2--0.8174 °2
S0.073 Å °-0.0808 Å °-0.0234 Å °0.0381 Å °-0.0422 Å °0.0368 Å °-0.1343 Å °0.0525 Å °-0.0308 Å °

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