[English] 日本語
Yorodumi
- PDB-5m6u: HUMAN PI3KDELTA IN COMPLEX WITH LASW1579 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m6u
TitleHUMAN PI3KDELTA IN COMPLEX WITH LASW1579
Components
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
KeywordsTRANSFERASE / PI3KDELTA KINASE / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


B cell chemotaxis / mast cell differentiation / mast cell chemotaxis / natural killer cell differentiation / perinuclear endoplasmic reticulum membrane / positive regulation of epithelial tube formation / natural killer cell chemotaxis / regulation of toll-like receptor 4 signaling pathway / neutrophil extravasation / positive regulation of neutrophil apoptotic process ...B cell chemotaxis / mast cell differentiation / mast cell chemotaxis / natural killer cell differentiation / perinuclear endoplasmic reticulum membrane / positive regulation of epithelial tube formation / natural killer cell chemotaxis / regulation of toll-like receptor 4 signaling pathway / neutrophil extravasation / positive regulation of neutrophil apoptotic process / phosphatidylinositol kinase activity / respiratory burst involved in defense response / phosphatidylinositol 3-kinase regulator activity / IRS-mediated signalling / positive regulation of focal adhesion disassembly / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / T cell chemotaxis / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / kinase activator activity / natural killer cell activation / transmembrane receptor protein tyrosine kinase adaptor activity / RHOF GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of endoplasmic reticulum unfolded protein response / RHOD GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol 3-kinase complex / enzyme-substrate adaptor activity / Nephrin family interactions / Signaling by LTK in cancer / Costimulation by the CD28 family / RND1 GTPase cycle / Signaling by LTK / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / positive regulation of leukocyte migration / PI3K/AKT activation / RND2 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / positive regulation of filopodium assembly / RND3 GTPase cycle / growth hormone receptor signaling pathway / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / phosphatidylinositol 3-kinase / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / natural killer cell mediated cytotoxicity / 1-phosphatidylinositol-3-kinase activity / RHOV GTPase cycle / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / mast cell degranulation / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / RHOC GTPase cycle / RHOJ GTPase cycle / intracellular glucose homeostasis / negative regulation of osteoclast differentiation / B cell activation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CD28 dependent PI3K/Akt signaling / RHOU GTPase cycle / CDC42 GTPase cycle / PI3K events in ERBB2 signaling / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / T cell differentiation / RHOG GTPase cycle / PI3K Cascade / extrinsic apoptotic signaling pathway via death domain receptors / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / GAB1 signalosome / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / phosphatidylinositol 3-kinase binding / positive regulation of lamellipodium assembly / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants
Similarity search - Function
PI3Kdelta, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kdelta, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Rho GTPase activation protein / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-7KA / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform / Phosphatidylinositol 3-kinase regulatory subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSegarra, V. / Hernandez, B. / Lozoya, E. / Blaesse, M. / Hoeppner, S. / Jestel, A.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Discovery of a Potent, Selective, and Orally Available PI3K delta Inhibitor for the Treatment of Inflammatory Diseases.
Authors: Erra, M. / Taltavull, J. / Greco, A. / Bernal, F.J. / Caturla, J.F. / Gracia, J. / Dominguez, M. / Sabate, M. / Paris, S. / Soria, S. / Hernandez, B. / Armengol, C. / Cabedo, J. / Bravo, M. ...Authors: Erra, M. / Taltavull, J. / Greco, A. / Bernal, F.J. / Caturla, J.F. / Gracia, J. / Dominguez, M. / Sabate, M. / Paris, S. / Soria, S. / Hernandez, B. / Armengol, C. / Cabedo, J. / Bravo, M. / Calama, E. / Miralpeix, M. / Lehner, M.D.
History
DepositionOct 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,7693
Polymers199,3972
Non-polymers3721
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area50870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.493, 113.212, 144.321
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform / PtdIns-3-kinase subunit delta / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic ...PtdIns-3-kinase subunit delta / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit delta / p110delta


Mass: 115728.586 Da / Num. of mol.: 1 / Fragment: N-terminal truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CD / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O00329, phosphatidylinositol-4,5-bisphosphate 3-kinase
#2: Protein Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


Mass: 83668.180 Da / Num. of mol.: 1 / Fragment: UNP residues 431-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3R1, GRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27986
#3: Chemical ChemComp-7KA / 4-azanyl-6-[[(1~{S})-1-(4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]pyrimidine-5-carbonitrile


Mass: 372.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16N8O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NULL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.85→89.08 Å / Num. obs: 36112 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WXR

2wxr


Resolution: 2.85→89.08 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.895 / SU B: 37.838 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.984 / ESU R Free: 0.416
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3089 997 2.8 %RANDOM
Rwork0.2555 ---
obs0.2569 35097 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 236.36 Å2 / Biso mean: 110.982 Å2 / Biso min: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.85→89.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8811 0 28 0 8839
Biso mean--95.56 --
Num. residues----1080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217909
X-RAY DIFFRACTIONr_bond_other_d0.0020.025581
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.94810716
X-RAY DIFFRACTIONr_angle_other_deg0.968312932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.38651071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20523.603297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.109151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1071539
X-RAY DIFFRACTIONr_chiral_restr0.0590.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219200
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021649
X-RAY DIFFRACTIONr_mcbond_it1.23425418
X-RAY DIFFRACTIONr_mcbond_other0.22322166
X-RAY DIFFRACTIONr_mcangle_it2.15638401
X-RAY DIFFRACTIONr_scbond_it3.51342491
X-RAY DIFFRACTIONr_scangle_it5.44662315
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 73 -
Rwork0.277 2560 -
all-2633 -
obs--100 %
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)
13.21011.7614-2.03915.4921-2.30976.5114-0.1816-0.14310.29790.40360.1658-0.1693-0.1226-0.02310.01590.5002-0.0915-0.01130.4736-0.00670.2108000
22.94940.4985-0.95823.94190.54096.82140.40270.08731.07090.27840.0324-0.0824-1.91520.2227-0.4351.08480.04160.2220.63810.13840.7635000
33.36380.4816-0.71564.9815-0.37233.12470.03630.3676-0.711-0.4828-0.18950.65520.6054-0.3930.15330.8809-0.0639-0.04290.831-0.20210.5451000
44.9105-0.7973-1.33471.83320.13632.3894-0.07050.4688-0.5895-0.0140.00340.70250.1292-0.76390.06710.55120.04870.0080.66890.02320.4893000
54.29470.4267-2.53513.9584-0.71085.80740.0544-0.42440.17850.2248-0.0474-1.087-0.31691.1477-0.0070.5753-0.0289-0.05730.65040.04560.5773000
66.1061.06740.23953.0201-0.36357.0840.229-1.071200.9329-0.0826-0.289-0.37170.729-0.14640.9004-0.01-0.03290.67240.02950.3552000
71.71371.8299-3.24581.9577-3.79628.2679-0.1665-0.1644-0.2319-0.2456-0.1826-0.26910.21630.2810.34910.89-0.06340.15750.5638-0.03710.3688000
83.21011.7614-2.03915.4921-2.30976.5114-0.1816-0.14310.29790.40360.1658-0.1693-0.1226-0.02310.01590.5002-0.0915-0.01130.4736-0.00670.210842.81418.786-11.327
92.94940.4985-0.95823.94190.54096.82140.40270.08731.07090.27840.0324-0.0824-1.91520.2227-0.4351.08480.04160.2220.63810.13840.763520.77633.01516.098
103.36380.4816-0.71564.9815-0.37233.12470.03630.3676-0.711-0.4828-0.18950.65520.6054-0.3930.15330.8809-0.0639-0.04290.831-0.20210.54515.431-8.0658.184
114.9105-0.7973-1.33471.83320.13632.3894-0.07050.4688-0.5895-0.0140.00340.70250.1292-0.76390.06710.55120.04870.0080.66890.02320.4893-0.83211.87517.901
124.29470.4267-2.53513.9584-0.71085.80740.0544-0.42440.17850.2248-0.0474-1.087-0.31691.1477-0.0070.5753-0.0289-0.05730.65040.04560.577334.18318.524.258
136.1061.06740.23953.0201-0.36357.0840.229-1.071200.9329-0.0826-0.289-0.37170.729-0.14640.9004-0.01-0.03290.67240.02950.355220.43314.06345.301
141.72521.8129-3.24891.9827-3.79168.2687-0.168-0.1652-0.2334-0.2434-0.1815-0.26690.21670.28120.34950.8902-0.06330.15770.5639-0.0370.36930.29-7.8937.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2A109 - 278
3X-RAY DIFFRACTION3A279 - 474
4X-RAY DIFFRACTION4A475 - 675
5X-RAY DIFFRACTION5A676 - 830
6X-RAY DIFFRACTION6A831 - 1050
7X-RAY DIFFRACTION7B1 - 1000
8X-RAY DIFFRACTION1A1 - 108
9X-RAY DIFFRACTION2A109 - 278
10X-RAY DIFFRACTION3A279 - 474
11X-RAY DIFFRACTION4A475 - 675
12X-RAY DIFFRACTION5A676 - 830
13X-RAY DIFFRACTION6A831 - 1050
14X-RAY DIFFRACTION7B1 - 1000

+
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