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- PDB-1fmk: CRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC -

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Basic information

Entry
Database: PDB / ID: 1fmk
TitleCRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC
ComponentsTYROSINE-PROTEIN KINASE SRC
KeywordsPHOSPHOTRANSFERASE / SRC / TYROSINE KINASE / PHOSPHORYLATION / SH2 / SH3 / PHOSPHOTYROSINE / PROTO-ONCOGENE
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity ...regulation of caveolin-mediated endocytosis / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of toll-like receptor 3 signaling pathway / regulation of cell projection assembly / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / negative regulation of telomere maintenance / Regulation of gap junction activity / ERBB2 signaling pathway / positive regulation of protein processing / positive regulation of integrin activation / BMP receptor binding / negative regulation of focal adhesion assembly / Activated NTRK2 signals through FYN / intestinal epithelial cell development / regulation of intracellular estrogen receptor signaling pathway / Netrin mediated repulsion signals / negative regulation of neutrophil activation / positive regulation of small GTPase mediated signal transduction / focal adhesion assembly / connexin binding / osteoclast development / cellular response to fluid shear stress / Activated NTRK3 signals through PI3K / signal complex assembly / regulation of vascular permeability / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / EPH-Ephrin signaling / podosome / positive regulation of podosome assembly / positive regulation of lamellipodium morphogenesis / DCC mediated attractive signaling / regulation of bone resorption / Regulation of RUNX1 Expression and Activity / Ephrin signaling / Signal regulatory protein family interactions / odontogenesis / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / leukocyte migration / Regulation of KIT signaling / cellular response to peptide hormone stimulus / regulation of early endosome to late endosome transport / Signaling by ALK / canonical glycolysis / phospholipase activator activity / EPHA-mediated growth cone collapse / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / Receptor Mediated Mitophagy / positive regulation of Notch signaling pathway / Signaling by EGFR / oogenesis / stimulatory C-type lectin receptor signaling pathway / RUNX2 regulates osteoblast differentiation / Fc-gamma receptor signaling pathway involved in phagocytosis / forebrain development / uterus development / PECAM1 interactions / negative regulation of intrinsic apoptotic signaling pathway / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / progesterone receptor signaling pathway / Recycling pathway of L1 / regulation of heart rate by cardiac conduction / signaling receptor activator activity / FCGR activation / protein tyrosine kinase activator activity / RET signaling / negative regulation of anoikis / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / Long-term potentiation / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / GAB1 signalosome / negative regulation of hippo signaling / Nuclear signaling by ERBB4 / positive regulation of Rac protein signal transduction / negative regulation of protein-containing complex assembly / ephrin receptor binding / phospholipase binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / Signaling by ERBB2 / Integrin signaling / p38MAPK events / peptidyl-tyrosine phosphorylation / EPHB-mediated forward signaling / positive regulation of TORC1 signaling / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / Src homology 2 domains / SH2 domain ...SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / SH3 type barrels. / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MULTIPLE ISOMORPHOUS HEAVY-ATOM REPLACEMENT (MIR) METHOD. THREE DERIVATIVES USED FOR PHASING. / Resolution: 1.5 Å
AuthorsXu, W. / Harrison, S.C. / Eck, M.J.
CitationJournal: Nature / Year: 1997
Title: Three-dimensional structure of the tyrosine kinase c-Src.
Authors: Xu, W. / Harrison, S.C. / Eck, M.J.
History
DepositionJan 24, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYROSINE-PROTEIN KINASE SRC


Theoretical massNumber of molelcules
Total (without water)51,7101
Polymers51,7101
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.759, 87.380, 101.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYROSINE-PROTEIN KINASE SRC / C-SRC / P60-SRC


Mass: 51709.570 Da / Num. of mol.: 1
Fragment: RESIDUES 86-836, CONTAINING SH2, SH3, KINASE 2 DOMAINS AND C-TERMINAL TAIL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: P12931, EC: 2.7.1.112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMPIPES1reservoir
30.8 Msodium tartrate1reservoir
420 mMdithiothreitol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 48728 / % possible obs: 66.1 % / Rsym value: 0.049
Reflection
*PLUS
Num. obs: 25752 / % possible obs: 90 % / Num. measured all: 102852 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MULTIPLE ISOMORPHOUS HEAVY-ATOM REPLACEMENT (MIR) METHOD. THREE DERIVATIVES USED FOR PHASING.
Resolution: 1.5→20 Å
RfactorNum. reflection% reflection
Rfree0.264 -5 %
Rwork0.21 --
obs0.21 165384 -
Displacement parametersBiso mean: 28.3 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 0 490 6270
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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