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- PDB-5j5t: GLK co-crystal structure with aminopyrrolopyrimidine inhibitor -

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Basic information

Entry
Database: PDB / ID: 5j5t
TitleGLK co-crystal structure with aminopyrrolopyrimidine inhibitor
ComponentsMitogen-activated protein kinase kinase kinase kinase 3
KeywordsTransferase/Transferase Inhibitor / Protein kinsae / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


MAP kinase kinase kinase kinase activity / protein serine/threonine kinase activity => GO:0004674 / response to tumor necrosis factor / response to UV / JNK cascade / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity ...MAP kinase kinase kinase kinase activity / protein serine/threonine kinase activity => GO:0004674 / response to tumor necrosis factor / response to UV / JNK cascade / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6G2 / Mitogen-activated protein kinase kinase kinase kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSilvian, L.F. / Marcotte, D.
CitationJournal: Protein Sci. / Year: 2017
Title: Germinal-center kinase-like kinase co-crystal structure reveals a swapped activation loop and C-terminal extension.
Authors: Marcotte, D. / Rushe, M. / M Arduini, R. / Lukacs, C. / Atkins, K. / Sun, X. / Little, K. / Cullivan, M. / Paramasivam, M. / Patterson, T.A. / Hesson, T. / D McKee, T. / May-Dracka, T.L. / ...Authors: Marcotte, D. / Rushe, M. / M Arduini, R. / Lukacs, C. / Atkins, K. / Sun, X. / Little, K. / Cullivan, M. / Paramasivam, M. / Patterson, T.A. / Hesson, T. / D McKee, T. / May-Dracka, T.L. / Xin, Z. / Bertolotti-Ciarlet, A. / Bhisetti, G.R. / Lyssikatos, J.P. / Silvian, L.F.
History
DepositionApr 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Mitogen-activated protein kinase kinase kinase kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5932
Polymers42,2261
Non-polymers3671
Water43224
1
A: Mitogen-activated protein kinase kinase kinase kinase 3
hetero molecules

A: Mitogen-activated protein kinase kinase kinase kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1874
Polymers84,4522
Non-polymers7352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4750 Å2
ΔGint-36 kcal/mol
Surface area30510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.703, 63.324, 64.916
Angle α, β, γ (deg.)90.00, 116.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase kinase 3 / Germinal center kinase-related protein kinase / GLK / MAPK/ERK kinase kinase kinase 3 / MEKKK 3


Mass: 42225.973 Da / Num. of mol.: 1 / Fragment: UNP residues 13-380 / Mutation: S170A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K3, RAB8IPL1 / Production host: unidentified baculovirus
References: UniProt: Q8IVH8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6G2 / 5-[2-(piperidin-4-yl)-1,3-thiazol-5-yl]-3-[(pyridin-4-yl)methoxy]pyridin-2-amine


Mass: 367.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N5OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.8M Ammonium Sulfate, 0.1M BisTRIS pH 5.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2015
RadiationMonochromator: Diamond(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 7960 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 43.8 Å2 / Net I/σ(I): 5.8
Reflection shellResolution: 2.85→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.732 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 40B0

40b0


Resolution: 2.85→41.647 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 381 4.79 %RANDOM SELECTION
Rwork0.175 ---
obs0.1766 7960 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→41.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 26 24 2378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032418
X-RAY DIFFRACTIONf_angle_d0.6763277
X-RAY DIFFRACTIONf_dihedral_angle_d13.164878
X-RAY DIFFRACTIONf_chiral_restr0.024355
X-RAY DIFFRACTIONf_plane_restr0.004419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8502-3.26250.24541110.19362526X-RAY DIFFRACTION100
3.2625-4.10990.22011340.17172514X-RAY DIFFRACTION100
4.1099-41.65140.18131360.16992539X-RAY DIFFRACTION99

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