[English] 日本語
Yorodumi
- PDB-1ksw: Structure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ksw
TitleStructure of Human c-Src Tyrosine Kinase (Thr338Gly Mutant) in Complex with N6-benzyl ADP
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
KeywordsTRANSFERASE / SH3 / SH2 / Kinase / bump hole / bump-hole / chemical genetics / orthogonal substrate / ATP
Function / homology
Function and homology information


regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway ...regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to progesterone stimulus / positive regulation of dephosphorylation / regulation of cell projection assembly / negative regulation of telomere maintenance / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / ERBB2 signaling pathway / Regulation of gap junction activity / BMP receptor binding / negative regulation of focal adhesion assembly / positive regulation of integrin activation / Activated NTRK2 signals through FYN / positive regulation of protein processing / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / negative regulation of neutrophil activation / regulation of vascular permeability / focal adhesion assembly / osteoclast development / connexin binding / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / signal complex assembly / positive regulation of small GTPase mediated signal transduction / branching involved in mammary gland duct morphogenesis / Co-stimulation by CD28 / Regulation of RUNX1 Expression and Activity / DCC mediated attractive signaling / EPH-Ephrin signaling / positive regulation of podosome assembly / regulation of bone resorption / positive regulation of lamellipodium morphogenesis / Ephrin signaling / Signal regulatory protein family interactions / podosome / odontogenesis / negative regulation of mitochondrial depolarization / MET activates PTK2 signaling / cellular response to peptide hormone stimulus / Regulation of KIT signaling / regulation of early endosome to late endosome transport / leukocyte migration / Signaling by ALK / phospholipase activator activity / oogenesis / GP1b-IX-V activation signalling / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Receptor Mediated Mitophagy / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / stress fiber assembly / positive regulation of Notch signaling pathway / Signaling by EGFR / RUNX2 regulates osteoblast differentiation / stimulatory C-type lectin receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of cell-cell adhesion / Recycling pathway of L1 / PECAM1 interactions / uterus development / regulation of heart rate by cardiac conduction / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / protein tyrosine kinase activator activity / negative regulation of anoikis / signaling receptor activator activity / RET signaling / Long-term potentiation / FCGR activation / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / positive regulation of protein serine/threonine kinase activity / GAB1 signalosome / negative regulation of hippo signaling / vascular endothelial growth factor receptor signaling pathway / ephrin receptor signaling pathway / bone resorption / negative regulation of protein-containing complex assembly / forebrain development / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / phospholipase binding / T cell costimulation / cellular response to platelet-derived growth factor stimulus / p38MAPK events / ephrin receptor binding / Signaling by ERBB2 / EPHB-mediated forward signaling / Integrin signaling / ionotropic glutamate receptor binding / positive regulation of TORC1 signaling / NCAM signaling for neurite out-growth / substrate adhesion-dependent cell spreading / Downstream signal transduction
Similarity search - Function
SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...SH2 domain / SHC Adaptor Protein / SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / 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 / 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
N6-BENZYL ADENOSINE-5'-DIPHOSPHATE / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWitucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M.
CitationJournal: Chem.Biol. / Year: 2002
Title: Mutant tyrosine kinases with unnatural nucleotide specificity retain the structure and phospho-acceptor specificity of the wild-type enzyme.
Authors: Witucki, L.A. / Huang, X. / Shah, K. / Liu, Y. / Kyin, S. / Eck, M.J. / Shokat, K.M.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1832
Polymers51,6661
Non-polymers5171
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.81, 87.68, 106.28
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC / C-SRC


Mass: 51665.520 Da / Num. of mol.: 1 / Fragment: SH3, SH2 and Kinase domains / Mutation: T338G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical ChemComp-NBS / N6-BENZYL ADENOSINE-5'-DIPHOSPHATE


Mass: 517.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 4000, 50mM PIPES pH 6.5, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-15 mg/mlprotein1drop
220 mMHEPES1droppH7.6
3100 mM1dropNaCl
410 mMdithiothreitol1drop
51 mMN6-(benzyl)ADP1drop
650 mMPIPES1reservoirpH6.5
712 %PEG40001reservoir
810 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 12715 / Num. obs: 12715 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.071
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 46549 / Rmerge(I) obs: 0.071

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2SRC

2src


Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.294 -random 5%
Rwork0.231 --
all-12715 -
obs-12715 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 34 46 3691
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.771
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more