[English] 日本語
Yorodumi
- PDB-5kmo: TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kmo
TitleTrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(2-pyridyl)urea
ComponentsHigh affinity nerve growth factor receptor
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / juxtamembrane / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation ...behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / Retrograde neurotrophin signalling / nerve growth factor binding / NGF-independant TRKA activation / sympathetic nervous system development / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / response to axon injury / neuron development / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / cellular response to nerve growth factor stimulus / axon guidance / receptor protein-tyrosine kinase / positive regulation of GTPase activity / kinase binding / positive regulation of neuron projection development / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / early endosome / learning or memory / positive regulation of ERK1 and ERK2 cascade / receptor complex / endosome membrane / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein phosphorylation / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Leucine rich repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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-6UM / High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.67 Å
AuthorsSu, H.P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
Authors: Su, H.P. / Rickert, K. / Burlein, C. / Narayan, K. / Bukhtiyarova, M. / Hurzy, D.M. / Stump, C.A. / Zhang, X. / Reid, J. / Krasowska-Zoladek, A. / Tummala, S. / Shipman, J.M. / Kornienko, M. ...Authors: Su, H.P. / Rickert, K. / Burlein, C. / Narayan, K. / Bukhtiyarova, M. / Hurzy, D.M. / Stump, C.A. / Zhang, X. / Reid, J. / Krasowska-Zoladek, A. / Tummala, S. / Shipman, J.M. / Kornienko, M. / Lemaire, P.A. / Krosky, D. / Heller, A. / Achab, A. / Chamberlin, C. / Saradjian, P. / Sauvagnat, B. / Yang, X. / Ziebell, M.R. / Nickbarg, E. / Sanders, J.M. / Bilodeau, M.T. / Carroll, S.S. / Lumb, K.J. / Soisson, S.M. / Henze, D.A. / Cooke, A.J.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: High affinity nerve growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5722
Polymers37,2671
Non-polymers3051
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.810, 51.810, 229.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

-
Components

#1: Protein High affinity nerve growth factor receptor / Neurotrophic tyrosine kinase receptor type 1 / TRK1-transforming tyrosine kinase protein / ...Neurotrophic tyrosine kinase receptor type 1 / TRK1-transforming tyrosine kinase protein / Tropomyosin-related kinase A / Tyrosine kinase receptor / Tyrosine kinase receptor A / Trk-A / gp140trk / p140-TrkA


Mass: 37266.746 Da / Num. of mol.: 1
Fragment: catalytic domain with juxtamembrane region, UNP resdiues 376-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK1, MTC, TRK, TRKA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04629, receptor protein-tyrosine kinase
#2: Chemical ChemComp-6UM / 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-pyridin-2-yl-urea


Mass: 305.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.39 Å3/Da / Density % sol: 48.46 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.672→44.866 Å / Num. all: 10453 / Num. obs: 10453 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 54.45 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.166 / Rsym value: 0.149 / Net I/av σ(I): 3.905 / Net I/σ(I): 12.7 / Num. measured all: 101199
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.67-2.8210.20.4631.61529814930.160.5130.4635.2100
2.82-2.9910.10.3721.91431014220.130.4110.3726.5100
2.99-3.199.70.2662.71302413450.0950.2950.2668.9100
3.19-3.459.60.23.41205312550.0720.2240.211.3100
3.45-3.789.80.1484.51118411360.0520.1630.14815100
3.78-4.239.70.1225.21020410500.0430.1360.12217.9100
4.23-4.8890.1065.684159350.0390.1180.10619100
4.88-5.989.60.16.276888050.0350.110.119100
5.98-8.459.20.0936.658776370.0330.1010.09319.6100
8.45-44.8668.40.0885.431463750.0330.0980.08821.399.5

-
Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.67→44.87 Å / Cor.coef. Fo:Fc: 0.9164 / Cor.coef. Fo:Fc free: 0.8548 / SU R Cruickshank DPI: 0.74 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.741 / SU Rfree Blow DPI: 0.301 / SU Rfree Cruickshank DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 500 4.81 %RANDOM
Rwork0.1935 ---
obs0.1959 10402 99.76 %-
Displacement parametersBiso max: 132.58 Å2 / Biso mean: 40.63 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.3002 Å20 Å20 Å2
2---0.3002 Å20 Å2
3---0.6004 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: final / Resolution: 2.67→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 23 22 2319
Biso mean--27.63 31.06 -
Num. residues----291
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d790SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC8
X-RAY DIFFRACTIONt_gen_planes371HARMONIC8
X-RAY DIFFRACTIONt_it2355HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion288SEMIHARMONIC5
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_contact2617SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2355HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3193HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.11
X-RAY DIFFRACTIONt_other_torsion19.87
LS refinement shellResolution: 2.67→2.98 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2997 133 4.6 %
Rwork0.2132 2758 -
all0.2171 2891 -
obs--99.76 %

+
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