[English] 日本語
Yorodumi
- PDB-6h8s: CRYSTAL STRUCTURE OF THE MOUSE PROTEIN TYROSINE PHOSPHATASE PTPN5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h8s
TitleCRYSTAL STRUCTURE OF THE MOUSE PROTEIN TYROSINE PHOSPHATASE PTPN5 (STEP) IN COMPLEX WITH COMPOUND BI-0314
ComponentsTyrosine-protein phosphatase non-receptor type 5
KeywordsHYDROLASE / PROTEIN PHOSPHATASE / PTN5 / STEP / ALLOSTERIC MODULATOR
Function / homology
Function and homology information


: / positive regulation of response to drug / proximal dendrite / mitogen-activated protein kinase binding / positive regulation of protein targeting to mitochondrion / exploration behavior / positive regulation of receptor internalization / peptidyl-tyrosine dephosphorylation / response to immobilization stress / glutamate receptor binding ...: / positive regulation of response to drug / proximal dendrite / mitogen-activated protein kinase binding / positive regulation of protein targeting to mitochondrion / exploration behavior / positive regulation of receptor internalization / peptidyl-tyrosine dephosphorylation / response to immobilization stress / glutamate receptor binding / phosphotyrosine residue binding / protein dephosphorylation / protein-tyrosine-phosphatase / negative regulation of MAP kinase activity / synaptic membrane / protein tyrosine phosphatase activity / positive regulation of long-term synaptic potentiation / positive regulation of neuron projection development / positive regulation of protein import into nucleus / synaptic vesicle / perikaryon / membrane => GO:0016020 / positive regulation of protein phosphorylation / axon / neuronal cell body / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / identical protein binding / membrane / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...Protein-tyrosine phosphatase, receptor type R/non-receptor type 5 / Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-FSZ / Tyrosine-protein phosphatase non-receptor type 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.771 Å
AuthorsFiegen, D. / Schnapp, G.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule.
Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, ...Authors: Tautermann, C.S. / Binder, F. / Buttner, F.H. / Eickmeier, C. / Fiegen, D. / Gross, U. / Grundl, M.A. / Heilker, R. / Hobson, S. / Hoerer, S. / Luippold, A. / Mack, V. / Montel, F. / Peters, S. / Bhattacharya, S. / Vaidehi, N. / Schnapp, G. / Thamm, S. / Zeeb, M.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1672
Polymers34,8811
Non-polymers2861
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.303, 59.303, 181.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 5 / Neural-specific protein-tyrosine phosphatase / Striatum-enriched protein-tyrosine phosphatase / STEP


Mass: 34880.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptpn5 / Production host: Escherichia coli (E. coli) / References: UniProt: P54830, protein-tyrosine-phosphatase
#2: Chemical ChemComp-FSZ / 1-[3-piperidin-4-yl-5-(trifluoromethyl)phenyl]guanidine


Mass: 286.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17F3N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 26% PEG 3350, 0.1 M Tris pH 7.8, 0.2 M ammonium citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.771→56.3745 Å / Num. obs: 25620 / % possible obs: 78.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 21.69 Å2 / Rmerge(I) obs: 0.212 / Rsym value: 0.212 / Net I/σ(I): 11.4
Reflection shellResolution: 1.771→1.927 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1.5 / Rsym value: 1.793 / % possible all: 18

-
Processing

Software
NameVersionClassification
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
BUSTER2.11.7refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BIJ

2bij


Resolution: 1.771→28.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1255 4.9 %RANDOM
Rwork0.181 ---
obs0.183 25606 78.7 %-
Displacement parametersBiso mean: 27.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.5367 Å20 Å20 Å2
2--0.5367 Å20 Å2
3----1.0734 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.771→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 20 277 2670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082512HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963424HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d890SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2512HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion16.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion323SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3124SEMIHARMONIC4
LS refinement shellResolution: 1.77→1.87 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2478 -4.68 %
Rwork0.2432 489 -
all0.2435 513 -
obs--10.67 %
Refinement TLS params.Method: refined / Origin x: 1.9439 Å / Origin y: 25.3142 Å / Origin z: 18.2564 Å
111213212223313233
T-0.0788 Å2-0.0035 Å20.0026 Å2--0.0366 Å20.0015 Å2---0.0671 Å2
L1.007 °2-0.0567 °20.2583 °2-0.628 °2-0.2744 °2--1.5389 °2
S-0.0017 Å °0.005 Å °0.0832 Å °0.0293 Å °0.0052 Å °-0.0206 Å °0.0137 Å °0.0026 Å °-0.0035 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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