[English] 日本語
Yorodumi
- PDB-3pxk: FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH Pyrrolo[2,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pxk
TitleFOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH Pyrrolo[2,3-d]thiazole
ComponentsPTK2 protein
KeywordsTRANSFERASE / TYROSINE PROTEIN KINASE / ATP BINDING
Function / homology
Function and homology information


: / negative regulation of synapse assembly / : / central nervous system neuron axonogenesis / netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / negative regulation of axonogenesis / regulation of epithelial cell migration / negative regulation of organ growth ...: / negative regulation of synapse assembly / : / central nervous system neuron axonogenesis / netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / negative regulation of axonogenesis / regulation of epithelial cell migration / negative regulation of organ growth / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / nuclear migration / DCC mediated attractive signaling / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / negative regulation of cell-cell adhesion / positive regulation of cardiac muscle hypertrophy / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / endothelial cell migration / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / peptidyl-tyrosine autophosphorylation / EPHB-mediated forward signaling / extrinsic component of cytoplasmic side of plasma membrane / NCAM signaling for neurite out-growth / SH2 domain binding / extracellular matrix organization / Integrin signaling / negative regulation of autophagy / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / molecular function activator activity / cell motility / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / neuron migration / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / microtubule cytoskeleton organization / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / MAPK cascade / cell migration / integrin binding / lamellipodium / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / cell differentiation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / protein kinase activity / positive regulation of cell migration / positive regulation of protein phosphorylation / apical plasma membrane / signaling receptor binding / focal adhesion / innate immune response
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
Chem-PXK / Focal adhesion kinase 1 / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKoolman, H. / Heinrich, T. / Musil, D.
CitationJournal: To be Published
Title: Co-crystal Structures of FAK with an Unprecedented Pyrrolo[2,3-d]thiazole
Authors: Koolman, H. / Heinrich, T. / Musil, D.
History
DepositionDec 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Refinement description
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Feb 19, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 2.1Sep 13, 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: PTK2 protein
B: PTK2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1415
Polymers64,6082
Non-polymers5333
Water6,864381
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PTK2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5232
Polymers32,3041
Non-polymers2181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: PTK2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6193
Polymers32,3041
Non-polymers3142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.431, 50.873, 66.894
Angle α, β, γ (deg.)98.16, 101.98, 93.54
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein PTK2 protein /


Mass: 32304.221 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 410-689 / Mutation: P410G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI5
References: UniProt: Q8IYN9, UniProt: Q05397*PLUS, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PXK / 6-(4,4-dimethylpent-2-ynyl)-4~{H}-pyrrolo[2,3-d][1,3]thiazole


Mass: 218.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H14N2S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 0.1M Tris 16% PEG 3350 , pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→44.2 Å / Num. all: 54332 / Num. obs: 51111 / % possible obs: 94 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Biso Wilson estimate: 30.47 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 20
Reflection shellResolution: 1.79→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.2 / % possible all: 88.8

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MP8

1mp8


Resolution: 1.79→26.21 Å / Cor.coef. Fo:Fc: 0.9533 / Cor.coef. Fo:Fc free: 0.9372 / SU B: 6.475 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 2606 5.1 %RANDOM
Rwork0.1838 ---
obs0.1854 51102 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.1029 Å2-5.7246 Å20.8251 Å2
2---2.2618 Å24.7704 Å2
3---2.1589 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.79→26.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 35 381 4546
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014260HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995766HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1502SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes606HARMONIC5
X-RAY DIFFRACTIONt_it4260HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2533 167 5.2 %
Rwork0.2041 3046 -
all0.2066 3213 -
obs--93.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19050.8530.21541.83890.9831.44310.0383-0.06470.04680.0826-0.10690.12570.0107-0.06450.0686-0.07910.06-0.018-0.0796-0.0192-0.0791-2.9887-14.455515.1338
20.89770.0930.16611.47020.95281.48960.0353-0.00160.0286-0.18640.0432-0.05650.00010.1657-0.0785-0.07520.0695-0.0013-0.0157-0.0065-0.13713.778613.6681-14.0111
3-0.01020.04040.09080.01670.03790.0809-0.001-0.00980.00010.0002-0.00290.009-0.0023-0.00040.00390.0438-0.032-0.0333-0.0196-0.0347-0.0233-0.4459-5.346120.5955
40.0479-0.0065-0.01480.109-0.03550.0014-0.00020-0.0017-0.00340.00130.0030.00090.003-0.0010.0420.0221-0.08590.00220.0099-0.04270.84735.9337-20.5151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|415 - A|687 }A415 - 687
2X-RAY DIFFRACTION2{ B|414 - B|687 }B414 - 687
3X-RAY DIFFRACTION3{ A|701 - A|701 }A701
4X-RAY DIFFRACTION4{ B|702 - B|702 }B702

+
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