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- PDB-4w9w: Crystal Structure of BMP-2-inducible kinase in complex with small... -

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Basic information

Entry
Database: PDB / ID: 4w9w
TitleCrystal Structure of BMP-2-inducible kinase in complex with small molecule AZD-7762
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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...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 / phosphorylation / 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. / Protein kinase domain ...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
Chem-YDJ / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsSorrell, F.J. / Elkins, J.M. / Krojer, T. / Savitsky, P. / Williams, E. / 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

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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)35,3928
Polymers34,3571
Non-polymers1,0357
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint15 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.220, 112.730, 163.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Detailsbiological unit is the same as asym.

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Components

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


Mass: 34356.570 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 39-344 / Mutation: K320A, K321A
Source method: isolated from a genetically manipulated source
Details: Surface entropy mutant of BMP2K kinase domain (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-YDJ / 5-(3-fluorophenyl)-N-[(3S)-3-piperidyl]-3-ureido-thiophene-2-carboxamide


Mass: 362.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19FN4O2S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 4M sodium formate, 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 wavelength
IDWavelength (Å)Relative weight
10.921
20.921
ReflectionResolution: 1.72→33.34 Å / Num. obs: 41784 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Net I/σ(I): 15.1 / Num. measured all: 259371 / Scaling rejects: 31
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.72-1.7560.8721317121900.810.38299.9
9.1-33.346.10.03442.520583350.9990.01498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.72 Å33.34 Å
Translation1.72 Å33.34 Å

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1682)refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→33.34 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 2054 4.92 %
Rwork0.1662 --
obs0.1677 41766 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.94 Å2 / Biso mean: 37.9443 Å2 / Biso min: 17.42 Å2
Refinement stepCycle: final / Resolution: 1.72→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 70 232 2639
Biso mean--38.79 47.04 -
Num. residues----306
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)
14.30530.59131.14614.48860.73122.31420.08150.20490.6355-0.11660.1022-0.5715-0.49790.3668-0.08680.3498-0.0490.07990.222-0.03150.48621.349-9.412-43.0913
22.3925-0.66120.00623.36281.23171.92770.32120.60510.2783-0.4133-0.245-0.2184-0.5124-0.0285-0.0120.41940.07980.05270.30420.03980.3209-2.9488-16.9588-51.7401
31.1597-0.1821-0.2461.50080.72022.82450.00570.26590.0931-0.2126-0.06810.033-0.614-0.41190.01910.24530.0821-0.04140.2734-0.02430.1838-0.3245-30.6753-62.0754
42.431-0.3701-0.03911.91520.06223.1389-0.05210.3439-0.3361-0.0424-0.09580.04220.1438-0.26220.04410.1403-0.007-0.01330.2274-0.0790.22171.9236-44.3943-59.9251
50.43250.2115-0.4113.11060.29452.01790.0012-0.15660.1583-0.3996-0.19541.0182-0.0457-0.43130.28480.1873-0.0416-0.0460.3524-0.00020.4188-9.7698-58.8077-64.2949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 39:79)A39 - 79
2X-RAY DIFFRACTION2(chain A and resid 80:148)A80 - 148
3X-RAY DIFFRACTION3(chain A and resid 149:274)A149 - 274
4X-RAY DIFFRACTION4(chain A and resid 275:329)A275 - 329
5X-RAY DIFFRACTION5(chain A and resid 330:344)A330 - 344

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