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- PDB-1byg: KINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1byg
TitleKINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WITH INHIBITOR STAUROSPORINE
ComponentsPROTEIN (C-TERMINAL SRC KINASE)
KeywordsTRANSFERASE / PROTEIN KINASE / C-TERMINAL SRC KINASE / PHOSPHORYLATION / STAUROSPORINE
Function / homology
Function and homology information


negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of T cell activation / adherens junction organization / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / negative regulation of T cell receptor signaling pathway ...negative regulation of Golgi to plasma membrane protein transport / regulation of Fc receptor mediated stimulatory signaling pathway / negative regulation of T cell activation / adherens junction organization / proline-rich region binding / negative regulation of low-density lipoprotein particle clearance / negative regulation of bone resorption / cellular response to peptide hormone stimulus / negative regulation of phagocytosis / negative regulation of T cell receptor signaling pathway / Phosphorylation of CD3 and TCR zeta chains / protein kinase A catalytic subunit binding / negative regulation of interleukin-6 production / oligodendrocyte differentiation / RHOH GTPase cycle / Co-inhibition by PD-1 / GAB1 signalosome / T cell costimulation / Integrin signaling / Negative regulation of FLT3 / protein tyrosine kinase binding / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / negative regulation of ERK1 and ERK2 cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / T cell receptor signaling pathway / protein tyrosine kinase activity / protein phosphatase binding / adaptive immune response / protein phosphorylation / intracellular signal transduction / negative regulation of cell population proliferation / extracellular exosome / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CSK-like, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily ...CSK-like, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
STAUROSPORINE / Tyrosine-protein kinase CSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAntson, A.A. / Lamers, M.B.A.C. / Scott, R.K. / Williams, D.H. / Hubbard, R.E.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Structure of the protein tyrosine kinase domain of C-terminal Src kinase (CSK) in complex with staurosporine.
Authors: Lamers, M.B. / Antson, A.A. / Hubbard, R.E. / Scott, R.K. / Williams, D.H.
History
DepositionOct 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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

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Assembly

Deposited unit
A: PROTEIN (C-TERMINAL SRC KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6482
Polymers31,1821
Non-polymers4671
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.490, 120.580, 48.290
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 PROTEIN (C-TERMINAL SRC KINASE) / CSK


Mass: 31181.918 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE C-TERMINAL HISTIDINE TAG WAS NOT OBSERVED IN THE DENSITY AND IS NOT PRESENT IN THE SEQRES.
Source: (gene. exp.) Homo sapiens (human)
Description: THE CDNA FOR THE CATALYTIC DOMAIN OF CSK WAS ISOLATED BY POLYMERASE CHAIN REACTION FROM GRANULOCYTE CDNA OBTAINED FROM HUMAN LUNG TISSUE. A HEXAHISTIDINE TAG WAS ENGINEERED AT THE C- ...Description: THE CDNA FOR THE CATALYTIC DOMAIN OF CSK WAS ISOLATED BY POLYMERASE CHAIN REACTION FROM GRANULOCYTE CDNA OBTAINED FROM HUMAN LUNG TISSUE. A HEXAHISTIDINE TAG WAS ENGINEERED AT THE C-TERMINUS TO AID PURIFICATION.
Cell: GRANULOCYTE / Organ: LUNG / Plasmid: PQE60-CSK / Gene (production host): CSK / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P41240, EC: 2.7.1.112
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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 Å3/Da / Density % sol: 38 %
Crystal growpH: 9
Details: VAPOUR DIFFUSION, PROTEIN SOLUTION (10 MG/ML) CONTAINING 1MM STAUROSPORINE WAS MIXED IN 1:1 RATIO WITH THE RESERVOIR SOLUTION. THE RESERVOIR SOLUTION CONTAINED 0.2M MGCL2, 0.1M TRISHCL PH 9.0, 24% PEG 4000.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21 mMstaurosporine1drop
30.2 M1reservoirMgCl2
40.1 MTris-HCl1reservoirpH9.0
524 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 15, 1997 / Details: MIRROR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 30746 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / % possible all: 61.8
Reflection shell
*PLUS
% possible obs: 61.8 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FMK

1fmk


Resolution: 2.4→20 Å / SU B: 10.8 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1007 10 %RANDOM
Rwork0.199 ---
obs-10089 93.6 %-
Displacement parametersBiso mean: 43.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 35 152 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.2
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.341.5
X-RAY DIFFRACTIONp_mcangle_it2.292
X-RAY DIFFRACTIONp_scbond_it4.584
X-RAY DIFFRACTIONp_scangle_it5.976
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.2610.3
X-RAY DIFFRACTIONp_singtor_nbd0.1870.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.63
X-RAY DIFFRACTIONp_staggered_tor18.620
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor20.730
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 43.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.2
X-RAY DIFFRACTIONp_plane_restr0.02
X-RAY DIFFRACTIONp_chiral_restr0.3
X-RAY DIFFRACTIONp_mcbond_it1.51.34
X-RAY DIFFRACTIONp_scbond_it44.58
X-RAY DIFFRACTIONp_mcangle_it22.29
X-RAY DIFFRACTIONp_scangle_it65.97

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