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- PDB-1pkg: Structure of a c-Kit Kinase Product Complex -

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Basic information

Entry
Database: PDB / ID: 1pkg
TitleStructure of a c-Kit Kinase Product Complex
Componentsc-kit protein
KeywordsTRANSFERASE ACTIVATOR / kinase / autophosphorylation / transactivation
Function / homology
Function and homology information


Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants ...Dasatinib-resistant KIT mutants / Imatinib-resistant KIT mutants / KIT mutants bind TKIs / Masitinib-resistant KIT mutants / Nilotinib-resistant KIT mutants / Regorafenib-resistant KIT mutants / Signaling by kinase domain mutants of KIT / Sunitinib-resistant KIT mutants / Signaling by juxtamembrane domain KIT mutants / Sorafenib-resistant KIT mutants / Signaling by extracellular domain mutants of KIT / stem cell factor receptor activity / hematopoietic stem cell migration / melanocyte adhesion / positive regulation of pyloric antrum smooth muscle contraction / positive regulation of colon smooth muscle contraction / erythropoietin-mediated signaling pathway / positive regulation of vascular associated smooth muscle cell differentiation / melanocyte migration / positive regulation of dendritic cell cytokine production / Kit signaling pathway / regulation of bile acid metabolic process / positive regulation of small intestine smooth muscle contraction / mast cell differentiation / positive regulation of mast cell proliferation / mast cell chemotaxis / Fc receptor signaling pathway / glycosphingolipid metabolic process / mast cell proliferation / positive regulation of long-term neuronal synaptic plasticity / detection of mechanical stimulus involved in sensory perception of sound / positive regulation of pseudopodium assembly / immature B cell differentiation / melanocyte differentiation / positive regulation of mast cell cytokine production / lymphoid progenitor cell differentiation / germ cell migration / myeloid progenitor cell differentiation / digestive tract development / negative regulation of programmed cell death / embryonic hemopoiesis / lamellipodium assembly / tongue development / megakaryocyte development / Regulation of KIT signaling / pigmentation / stem cell population maintenance / mast cell degranulation / positive regulation of Notch signaling pathway / cytokine binding / negative regulation of reproductive process / negative regulation of developmental process / growth factor binding / somatic stem cell population maintenance / hemopoiesis / T cell differentiation / spermatid development / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / : / response to cadmium ion / ovarian follicle development / positive regulation of tyrosine phosphorylation of STAT protein / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SH2 domain binding / B cell differentiation / erythrocyte differentiation / cell chemotaxis / acrosomal vesicle / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / epithelial cell proliferation / stem cell differentiation / positive regulation of receptor signaling pathway via JAK-STAT / visual learning / Signaling by SCF-KIT / receptor protein-tyrosine kinase / cytoplasmic side of plasma membrane / fibrillar center / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / cell-cell junction / PIP3 activates AKT signaling / regulation of cell population proliferation / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / RAF/MAP kinase cascade / spermatogenesis / protein tyrosine kinase activity / protease binding / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / intracellular signal transduction / positive regulation of cell migration / inflammatory response
Similarity search - Function
Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...Mast/stem cell growth factor receptor / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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
ADENOSINE-5'-DIPHOSPHATE / Mast/stem cell growth factor receptor Kit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMol, C.D. / Lim, K.B. / Sridhar, V. / Zou, H. / Chien, E.Y.T. / Sang, B.-C. / Nowakowski, J. / Kassel, D.B. / Cronin, C.N. / McRee, D.E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of a c-Kit Product Complex Reveals the Basis for Kinase Transactivation.
Authors: Mol, C.D. / Lim, K.B. / Sridhar, V. / Zou, H. / Chien, E.Y.T. / Sang, B.-C. / Nowakowski, J. / Kassel, D.B. / Cronin, C.N. / McRee, D.E.
History
DepositionJun 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Remark 999SEQUENCE C-KIT IS A TYPE III RECEPTOR PROTEIN TYROSINE KINASE WITH A "SPLIT" KINASE DOMAIN, I.E. ...SEQUENCE C-KIT IS A TYPE III RECEPTOR PROTEIN TYROSINE KINASE WITH A "SPLIT" KINASE DOMAIN, I.E. THE TWO CONSERVED KINASE DOMAINS ARE INTERRUPTED BY A LARGE NON-CONSERVED INSERTION CALLED THE KINASE INSERTION DOMAIN (KID). IN THE CONSTRUCT THE KID RESIDUES 694-753 WERE DELETED AND REPLACED WITH TWO VECTOR RESIDUES (THR-SER).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: c-kit protein
B: c-kit protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0096
Polymers75,1062
Non-polymers9034
Water543
1
A: c-kit protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0053
Polymers37,5531
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: c-kit protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0053
Polymers37,5531
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: c-kit protein
B: c-kit protein
hetero molecules

A: c-kit protein
B: c-kit protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,01912
Polymers150,2134
Non-polymers1,8068
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10810 Å2
ΔGint-156 kcal/mol
Surface area50440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.667, 116.458, 60.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein c-kit protein


Mass: 37553.188 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10721
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: PEG, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
16 mg/mlenzyme1drop
2150 mM1dropNaCl
325 mMTris1droppH7.9
42.5 mMATP1drop
55 mM1dropMgCl2
618 %PEG80001reservoir
70.1 MMES1reservoirpH7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003 / Details: mirrors
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 14652
Reflection
*PLUS
Highest resolution: 2.9 Å / % possible obs: 97 % / Num. measured all: 49361 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.834 / SU B: 24.258 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31129 709 5 %RANDOM
Rwork0.22451 ---
all0.22874 ---
obs0.22874 13437 97.1 %-
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: 16.956 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2--2.5 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 56 3 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224730
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9836412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4655566
X-RAY DIFFRACTIONr_chiral_restr0.1090.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023484
X-RAY DIFFRACTIONr_nbd_refined0.2380.22343
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.28
X-RAY DIFFRACTIONr_mcbond_it0.4491.52843
X-RAY DIFFRACTIONr_mcangle_it0.8824578
X-RAY DIFFRACTIONr_scbond_it1.39831887
X-RAY DIFFRACTIONr_scangle_it2.3564.51834
LS refinement shellResolution: 2.9→2.969 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 59
Rwork0.323 914
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)
15.8135-3.4426-0.58334.43443.09772.98470.03280.2017-0.2007-0.2122-0.14090.2736-0.1022-0.13920.10820.11080.0006-0.0130.17950.02260.188216.029317.706424.637
25.21751.8901-1.0465.2975-0.32792.60070.0004-0.2282-0.2072-0.0432-0.0353-0.0434-0.09560.19610.03490.03570.0431-0.03090.0884-0.01570.039538.689521.509428.5596
38.6002-3.9066-4.56362.54922.40014.69970.1497-0.0960.2543-0.1603-0.1254-0.0556-0.1539-0.0537-0.02430.2654-0.0132-0.03770.17950.09610.131553.26121.251-0.5327
45.999-1.4950.00467.0316-1.50744.2460.02550.1827-0.0972-0.60670.0612-0.7110.19670.2305-0.08680.23080.03580.10210.18770.07530.173474.58134.1613-6.0469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA567 - 67519 - 127
2X-RAY DIFFRACTION2AA676 - 927128 - 321
3X-RAY DIFFRACTION3BB566 - 67518 - 127
4X-RAY DIFFRACTION4BB676 - 929128 - 323
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.31 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.61
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å

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