[English] 日本語
Yorodumi
- PDB-8sc8: Structure of PI3KG in complex with MTX-531 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sc8
TitleStructure of PI3KG in complex with MTX-531
ComponentsPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
KeywordsTRANSFERASE/INHIBITOR / PI3KG / dual EGFR/PI3K inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis ...secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / regulation of calcium ion transmembrane transport / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / dendritic cell chemotaxis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / positive regulation of Rac protein signal transduction / Synthesis of PIPs at the plasma membrane / regulation of cell adhesion mediated by integrin / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / T cell activation / neutrophil chemotaxis / ephrin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / phosphorylation / positive regulation of MAP kinase activity / positive regulation of cytokine production / platelet aggregation / G beta:gamma signalling through PI3Kgamma / endocytosis / kinase activity / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / angiogenesis / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / inflammatory response / immune response / G protein-coupled receptor signaling pathway / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain ...PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / 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. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.687 Å
AuthorsWhitehead, C.E. / Leopold, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of PI3KG in complex with MTX-531
Authors: Whitehead, C.E. / Leopold, J.
History
DepositionApr 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6617
Polymers110,7271
Non-polymers9346
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.934, 67.452, 106.983
Angle α, β, γ (deg.)90.000, 95.274, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / PtdIns-3-kinase subunit gamma / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic ...PtdIns-3-kinase subunit gamma / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit gamma / p110gamma / Phosphoinositide-3-kinase catalytic gamma polypeptide / Serine/threonine protein kinase PIK3CG / p120-PI3K


Mass: 110727.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CG / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48736, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-D0D / N-[(5P)-2-chloro-5-(4-{[(1R)-1-phenylethyl]amino}quinazolin-6-yl)pyridin-3-yl]methanesulfonamide


Mass: 453.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20ClN5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 0.2 M Lithium Sulfate, 0.1 M TRIS-HCl pH 8.2, 15% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 2.687→33.726 Å / Num. obs: 23452 / % possible obs: 91.6 % / Redundancy: 6.1 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.362 / Rmerge(I) obs: 0.0717 / Rpim(I) all: 0.0316 / Rrim(I) all: 0.0785 / AbsDiff over sigma anomalous: 0.692 / Baniso tensor eigenvalue 1: 23.0769 Å2 / Baniso tensor eigenvalue 2: 18.3309 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 0.8302 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.5575 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.5575 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.8302 / Aniso diffraction limit 1: 2.977 Å / Aniso diffraction limit 2: 2.734 Å / Aniso diffraction limit 3: 2.68 Å / Aniso diffraction limit axis 1 ortho1: 0.90037 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.43509 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.43509 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.90037 / Net I/σ(I): 13.96 / Num. measured all: 143017 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91 / % possible ellipsoidal: 91.6 / % possible ellipsoidal anomalous: 91 / % possible spherical: 81.6 / % possible spherical anomalous: 81 / Redundancy anomalous: 3.15 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.248-33.7265.480.032534.851284712847234423440.998-0.4770.01460.03570.60799.299.299.299.299.22.9399.2
4.94-6.2486.110.04929.151432914329234623460.996-0.4160.02150.05370.66599.710099.710099.73.18100
4.315-4.945.680.053625.721331213312234523450.996-0.2240.02470.05920.71599.499.799.499.799.42.9599.7
3.915-4.3155.990.079719.151404814048234523450.995-0.2330.03550.08750.7159910099100993.12100
3.631-3.9156.390.13512.721499414994234623460.99-0.1070.0580.14710.71799.699.999.699.999.63.2899.9
3.416-3.6316.520.23287.841528715287234423440.975-0.0050.09880.25330.71699.799.999.799.999.73.3599.9
3.242-3.4166.660.40444.631560615606234523450.9350.0260.16930.43890.70599.810099.810099.83.41100
3.101-3.2426.290.68142.61476714767234723470.820.0030.29510.74380.68799.810099.810099.83.23100
2.975-3.1015.811.04831.571362313623234423440.6440.0210.47591.15390.70295.595.795.595.795.52.9895.7
2.687-2.9756.051.22061.341420414204234623460.5470.0040.54141.33770.68853.153.753.131.331.13.153.7

-
Processing

Software
NameVersionClassification
autoPROC1.1.7 20220608data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
STARANISO2.3.87data scaling
REFMAC5.8.0352refinement
REFMAC5.8.0352phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.687→33.726 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 37.351 / SU ML: 0.351 / Cross valid method: FREE R-VALUE / ESU R Free: 0.412
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2533 1194 5.091 %
Rwork0.1951 22258 -
all0.198 --
obs-23452 81.564 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 98.219 Å2
Baniso -1Baniso -2Baniso -3
1--2.476 Å2-0 Å2-1.306 Å2
2--0.87 Å2-0 Å2
3---1.816 Å2
Refinement stepCycle: LAST / Resolution: 2.687→33.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 56 89 6853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0126914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166432
X-RAY DIFFRACTIONr_angle_refined_deg0.8121.6539361
X-RAY DIFFRACTIONr_angle_other_deg0.2831.57114984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.283540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.885101248
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.01310320
X-RAY DIFFRACTIONr_chiral_restr0.0370.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021357
X-RAY DIFFRACTIONr_nbd_refined0.1870.21428
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26370
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2165
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.29
X-RAY DIFFRACTIONr_nbd_other0.1160.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0380.22
X-RAY DIFFRACTIONr_mcbond_it2.5387.013302
X-RAY DIFFRACTIONr_mcbond_other2.5367.0113302
X-RAY DIFFRACTIONr_mcangle_it4.36710.4984110
X-RAY DIFFRACTIONr_mcangle_other4.36710.4984111
X-RAY DIFFRACTIONr_scbond_it2.1517.23612
X-RAY DIFFRACTIONr_scbond_other2.1517.2013613
X-RAY DIFFRACTIONr_scangle_it3.7210.7095251
X-RAY DIFFRACTIONr_scangle_other3.7210.715252
X-RAY DIFFRACTIONr_lrange_it6.76781.7497704
X-RAY DIFFRACTIONr_lrange_other6.76681.747703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.687-2.7560.50250.26875X-RAY DIFFRACTION3.8204
2.756-2.8310.264240.371318X-RAY DIFFRACTION16.6019
2.831-2.9130.417550.336847X-RAY DIFFRACTION45.88
2.913-3.0020.34720.3071437X-RAY DIFFRACTION78.5528
3.002-3.0990.335920.2861734X-RAY DIFFRACTION97.5949
3.099-3.2070.252880.2641761X-RAY DIFFRACTION100
3.207-3.3270.333990.2461634X-RAY DIFFRACTION100
3.327-3.4610.294900.2311617X-RAY DIFFRACTION99.9415
3.461-3.6140.287750.2171531X-RAY DIFFRACTION99.9378
3.614-3.7880.235800.1941483X-RAY DIFFRACTION99.9361
3.788-3.990.272680.1881434X-RAY DIFFRACTION99.9335
3.99-4.2280.216750.1631292X-RAY DIFFRACTION99.9269
4.228-4.5150.227660.1661255X-RAY DIFFRACTION99.6229
4.515-4.870.218620.1651172X-RAY DIFFRACTION99.8382
4.87-5.3230.236530.1821094X-RAY DIFFRACTION100
5.323-5.9330.223660.189961X-RAY DIFFRACTION100
5.933-6.8160.241470.204885X-RAY DIFFRACTION99.8928
6.816-8.2640.225340.179748X-RAY DIFFRACTION98.8622
8.264-11.3520.197240.144606X-RAY DIFFRACTION98.9011
11.352-33.7260.399190.214374X-RAY DIFFRACTION99.7462
Refinement TLS params.Method: refined / Origin x: 32.5494 Å / Origin y: -1.1008 Å / Origin z: 25.9238 Å
111213212223313233
T0.2863 Å2-0.0196 Å20.0763 Å2-0.0091 Å2-0.0094 Å2--0.0507 Å2
L3.7308 °20.6721 °20.6408 °2-0.5783 °20.1366 °2--1.3675 °2
S-0.0485 Å °-0.0078 Å °-0.2724 Å °0.0036 Å °0.058 Å °-0.0859 Å °-0.2369 Å °0.021 Å °-0.0095 Å °
Refinement TLS groupSelection: ALL

+
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://pdbjlc1.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