[English] 日本語
Yorodumi
- PDB-1o4m: CRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH MALONICACID. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o4m
TitleCRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH MALONICACID.
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE SRC
KeywordsSIGNALING PROTEIN / SH2 DOMAIN FRAGMENT APPROACH
Function / homology
Function and homology information


positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of ovarian follicle development / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / regulation of toll-like receptor 3 signaling pathway / positive regulation of ovarian follicle development / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / cellular response to prolactin / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / response to mineralocorticoid / positive regulation of dephosphorylation / ERBB2 signaling pathway / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of epithelial cell migration / positive regulation of protein transport / Regulation of gap junction activity / BMP receptor binding / positive regulation of lamellipodium morphogenesis / cellular response to progesterone stimulus / regulation of vascular permeability / positive regulation of protein processing / positive regulation of integrin activation / Activated NTRK2 signals through FYN / negative regulation of focal adhesion assembly / skeletal muscle cell proliferation / : / Netrin mediated repulsion signals / regulation of intracellular estrogen receptor signaling pathway / intestinal epithelial cell development / CD28 co-stimulation / positive regulation of glucose metabolic process / transcytosis / osteoclast development / Activated NTRK3 signals through PI3K / cellular response to fluid shear stress / response to acidic pH / connexin binding / focal adhesion assembly / signal complex assembly / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / positive regulation of podosome assembly / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / branching involved in mammary gland duct morphogenesis / adherens junction organization / DCC mediated attractive signaling / EPH-Ephrin signaling / odontogenesis / myoblast proliferation / Ephrin signaling / cellular response to peptide hormone stimulus / negative regulation of mitochondrial depolarization / podosome / Signal regulatory protein family interactions / cellular response to fatty acid / MET activates PTK2 signaling / regulation of early endosome to late endosome transport / Regulation of KIT signaling / postsynaptic specialization, intracellular component / Signaling by ALK / leukocyte migration / GP1b-IX-V activation signalling / CTLA4 inhibitory signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / phospholipase activator activity / oogenesis / Receptor Mediated Mitophagy / DNA biosynthetic process / EPHA-mediated growth cone collapse / p130Cas linkage to MAPK signaling for integrins / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / Signaling by EGFR / positive regulation of epithelial cell migration / stress fiber assembly / positive regulation of smooth muscle cell migration / stimulatory C-type lectin receptor signaling pathway / regulation of cell-cell adhesion / cellular response to platelet-derived growth factor stimulus / dendritic growth cone / regulation of heart rate by cardiac conduction / RUNX2 regulates osteoblast differentiation / Recycling pathway of L1 / uterus development / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / neurotrophin TRK receptor signaling pathway / phospholipase binding / negative regulation of telomere maintenance via telomerase / RHOU GTPase cycle / platelet-derived growth factor receptor signaling pathway / Long-term potentiation / negative regulation of anoikis / RET signaling / FCGR activation / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / positive regulation of bone resorption
Similarity search - Function
SH2 domain / SHC Adaptor Protein / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH2 domain / SHC Adaptor Protein / : / 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 / 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 / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 1.6 Å
AuthorsLange, G. / Loenze, P. / Liesum, A.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Requirements for specific binding of low affinity inhibitor fragments to the SH2 domain of (pp60)Src are identical to those for high affinity binding of full length inhibitors.
Authors: Lange, G. / Lesuisse, D. / Deprez, P. / Schoot, B. / Loenze, P. / Benard, D. / Marquette, J.P. / Broto, P. / Sarubbi, E. / Mandine, E.
History
DepositionJun 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)12,4792
Polymers12,3751
Non-polymers1041
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.551, 58.441, 64.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 12374.964 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC / Plasmid: BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P12931, EC: 2.7.1.112
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 41.9 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, sitting drop / Details: Lesuisse, D., (2002) J.Med.Chem., 45, 2379.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG4001reservoir
210 %DMSO1reservoir
3100 mMMES1reservoirpH5.5
410 mMdithiothreitol1reservoir
560-80 mg/mlprotein1drop
610 mMdithiothreitol1droppH5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 12907 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.073 / Net I/σ(I): 26
Reflection shellResolution: 1.6→1.65 Å / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 17 / % possible all: 80.8

-
Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: molecular replacement
Starting model: 1SHD

1shd


Resolution: 1.6→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 12907 96.3 %
Displacement parametersBiso mean: 17.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms848 0 7 166 1021
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_deg1.2
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

+
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