PDB-6aud: PI3K-gamma K802T in complex with Cpd 8 10-((1-(tert-butyl)piperid...

ID or keywords:

Entry

Database: PDB / ID: 6aud

Title

PI3K-gamma K802T in complex with Cpd 8 10-((1-(tert-butyl)piperidin-4-yl)sulfinyl)-2-(1-isopropyl-1H-1,2,4-triazol-5-yl)-5,6-dihydrobenzo[f]imidazo[1,2-d][1,4]oxazepine

Components

Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform

Keywords

TRANSFERASE/TRANSFERASE INHBITOR / p110 delta / SBDD / TRANSFERASE-TRANSFERASE INHBITOR complex

Function / homology

Function and homology information

negative regulation of triglyceride catabolic process / secretory granule localization / 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 / T cell chemotaxis / regulation of calcium ion transmembrane transport ...negative regulation of triglyceride catabolic process / secretory granule localization / 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 / T cell chemotaxis / regulation of calcium ion transmembrane transport / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / 1-phosphatidylinositol-4-phosphate 3-kinase activity / sphingosine-1-phosphate receptor signaling pathway / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / dendritic cell chemotaxis / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / phosphatidylinositol-mediated signaling / regulation of cell adhesion mediated by integrin / phosphatidylinositol phosphate biosynthetic process / Synthesis of PIPs at the plasma membrane / positive regulation of Rac protein signal transduction / regulation of angiogenesis / T cell proliferation / GPVI-mediated activation cascade / cellular response to cAMP / ephrin receptor binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / neutrophil chemotaxis / positive regulation of MAP kinase activity / T cell activation / positive regulation of cytokine production / platelet aggregation / endocytosis / G beta:gamma signalling through PI3Kgamma / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / adaptive immune response / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / immune response / G protein-coupled receptor signaling pathway / inflammatory response / innate immune response / protein serine kinase activity / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function

PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain ...PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / Phosphatidylinositol 3-kinase, accessory domain (PIK) / 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 / 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. / C2 domain / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.015 Å

Authors

Murray, J.M. / Ultsch, M.

Citation

Journal: ACS Med Chem Lett / Year: 2017
Title: Design of Selective Benzoxazepin PI3K delta Inhibitors Through Control of Dihedral Angles.
Authors: Safina, B.S. / Elliott, R.L. / Forrest, A.K. / Heald, R.A. / Murray, J.M. / Nonomiya, J. / Pang, J. / Salphati, L. / Seward, E.M. / Staben, S.T. / Ultsch, M. / Wei, B. / Yang, W. / Sutherlin, D.P.

History

Deposition	Aug 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: 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 viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6aud.cif.gz	364.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6aud.ent.gz	292.2 KB	Display	PDB format
PDBx/mmJSON format	6aud.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6aud_validation.pdf.gz	740.5 KB	Display	wwPDB validaton report
Full document	6aud_full_validation.pdf.gz	749.4 KB	Display
Data in XML	6aud_validation.xml.gz	32.8 KB	Display
Data in CIF	6aud_validation.cif.gz	47.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/au/6aud ftp://data.pdbj.org/pub/pdb/validation_reports/au/6aud	HTTPS FTP

-
Related structure data

Related structure data	3r7rS S: Starting model for refinement
Similar structure data	3dbs-d 3r7q-d 4anx-d 4ezj-d 3l08-d 4xx5-d 1e90-d 3qaq-d 1e8x-d 3l54-d 4ezk-d 3nzu-d 3r7r-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#148 - Apr 2012 Ras Protein similarity (35) #245 - May 2020 Spliceosomes similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform

hetero molecules

111 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	139.051, 66.065, 102.492
Angle α, β, γ (deg.)	90.00, 98.06, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1557- HOH
2	1	A-1589- HOH

Details

Monomer as determined bygel filtration

#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: 110699.023 Da / Num. of mol.: 1 / Fragment: p110 gamma, residues 144-1102 / Mutation: K802T 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-BWY / 10-[(S)-(1-tert-butylpiperidin-4-yl)sulfinyl]-2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine Mass: 482.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₅H₃₄N₆O₂S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.89 % / Mosaicity: 1.255 °
Crystal grow	Temperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 0.999 Å

Detector

Type: MACSCIENCE / Detector: CCD / Date: Aug 21, 2010

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.999 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 60464 / % possible obs: 99.9 % / Redundancy: 3.6 % / B_iso Wilson estimate: 33.06 Å² / R_merge(I) obs: 0.063 / Χ²: 1.028 / Net I/σ(I): 11.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2-2.07	3.5	0.555	5993	1.016	1	100
2.07-2.15	3.5	0.404	6006	1.042	1	100
2.15-2.25	3.5	0.313	6030	1.049	1	100
2.25-2.37	3.5	0.223	6040	1.041	1	100
2.37-2.52	3.5	0.17	6021	1.025	1	100
2.52-2.71	3.6	0.122	6035	1.033	1	100
2.71-2.99	3.7	0.085	6035	1.023	1	100
2.99-3.42	3.7	0.06	6066	1.02	1	99.9
3.42-4.31	3.7	0.048	6076	1.014	1	99.9
4.31-50	3.7	0.036	6162	1.019	1	99.3

-
Processing

Software

Name	Version	Classification
PHENIX	(1.12-2829_final)	refinement
DENZO		data reduction
SCALEPACK		data scaling
PDB_EXTRACT	3.22	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3r7r

3r7r

Resolution: 2.015→28.119 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.36 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2331	3017	4.99 %
R_work	0.2027	-	-
obs	0.2043	60446	99.09 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.015→28.119 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6796	0	34	290	7120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	6983
X-RAY DIFFRACTION	f_angle_d	0.593	9454
X-RAY DIFFRACTION	f_dihedral_angle_d	16.218	4199
X-RAY DIFFRACTION	f_chiral_restr	0.042	1062
X-RAY DIFFRACTION	f_plane_restr	0.004	1196

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.0149-2.0463	0.309	111	0.2804	2102	X-RAY DIFFRACTION	82
2.0463-2.0799	0.319	131	0.2667	2664	X-RAY DIFFRACTION	100
2.0799-2.1157	0.2637	139	0.2598	2584	X-RAY DIFFRACTION	100
2.1157-2.1542	0.2644	140	0.2515	2602	X-RAY DIFFRACTION	100
2.1542-2.1956	0.2992	129	0.2471	2665	X-RAY DIFFRACTION	100
2.1956-2.2404	0.2671	135	0.2501	2581	X-RAY DIFFRACTION	100
2.2404-2.2891	0.3057	137	0.2381	2645	X-RAY DIFFRACTION	100
2.2891-2.3423	0.2813	139	0.2232	2621	X-RAY DIFFRACTION	100
2.3423-2.4009	0.2785	123	0.2266	2653	X-RAY DIFFRACTION	100
2.4009-2.4657	0.2879	143	0.2316	2589	X-RAY DIFFRACTION	100
2.4657-2.5382	0.2592	142	0.2293	2641	X-RAY DIFFRACTION	100
2.5382-2.6201	0.2915	128	0.2291	2625	X-RAY DIFFRACTION	100
2.6201-2.7137	0.2837	124	0.2278	2645	X-RAY DIFFRACTION	100
2.7137-2.8222	0.2799	152	0.2294	2595	X-RAY DIFFRACTION	100
2.8222-2.9506	0.2262	141	0.2261	2640	X-RAY DIFFRACTION	100
2.9506-3.1059	0.2622	151	0.2259	2642	X-RAY DIFFRACTION	100
3.1059-3.3002	0.2439	125	0.212	2644	X-RAY DIFFRACTION	100
3.3002-3.5546	0.2346	149	0.1967	2609	X-RAY DIFFRACTION	100
3.5546-3.9115	0.2105	136	0.1761	2676	X-RAY DIFFRACTION	100
3.9115-4.4755	0.1849	160	0.166	2628	X-RAY DIFFRACTION	100
4.4755-5.6312	0.1999	142	0.1674	2648	X-RAY DIFFRACTION	100
5.6312-28.1214	0.1945	140	0.1796	2730	X-RAY DIFFRACTION	99

Refinement TLS params.

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

ID	L11 (°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)
1	0.5933	-0.4619	0.179	0.7651	0.2285	0.4692	0.0994	0.5107	-0.3895	-0.2409	-0.014	0.0321	0.4207	0.1279	0.0016	0.4332	0.038	-0.0412	0.3918	-0.017	0.3738	33.6206	-38.2775	7.721
2	2.1607	0.0982	0.615	1.953	-0.5508	2.1779	0.1327	-0.4345	-0.0345	0.2055	0.0401	0.3534	-0.0779	-0.7603	0.0139	0.3197	-0.0331	0.0803	0.5244	0.1112	0.4527	6.0114	-33.0973	32.4045
3	3.1376	0.2462	0.0162	0.7172	-0.2898	2.5899	0.0534	-0.2633	0.101	0.0722	-0.0565	0.0639	-0.0697	0.3311	-0.0001	0.2231	0.025	-0.0077	0.2808	-0.0397	0.218	60.2157	-22.873	12.1194
4	1.559	0.4464	-0.1583	0.4133	0.4737	0.9086	0.0028	-0.1897	-0.0306	-0.2121	-0.0536	0.2426	0.2706	0.1116	-0.0139	0.3542	0.0397	0.0487	0.3423	0.0206	0.2886	52.8618	-25.5946	10.2434
5	2.238	-0.2134	1.5525	0.1613	-0.1448	1.4775	0.0134	-0.3163	-0.1045	0.0715	0.01	-0.0482	0.0395	0.0015	0	0.2703	0.0357	0.0004	0.2854	0.0305	0.2814	41.8489	-30.7099	31.5402
6	1.5016	-1.3744	0.6186	2.0334	-0.8162	1.4914	-0.0257	0.1857	0.1006	-0.2487	0.0413	0.056	-0.2002	-0.0939	0.0004	0.3479	0.0067	-0.0299	0.3088	0.0328	0.3323	14.0051	-14.444	8.8709
7	0.7556	-0.008	0.4869	0.7883	0.3958	0.4514	-0.0876	0.0763	-0.2321	0.3863	-0.0608	0.1867	0.0662	0.0052	-0	0.3578	0.0563	0.0408	0.267	0.0196	0.2927	24.8379	-15.9339	32.5812
8	0.1295	-0.0694	0.1672	0.2189	0.0184	0.2125	-0.0503	0.1281	0.2697	-0.3596	0.1298	-0.2965	0.0072	0.4546	0	0.3175	0.0508	0.0232	0.2536	0.0195	0.3165	22.9547	-14.5983	16.2317
9	2.0161	-0.9143	0.3258	2.1889	-0.6019	2.0447	-0.0416	-0.1668	0.3078	0.23	0.0441	-0.2112	-0.3431	0.074	-0.002	0.3437	0.0143	-0.0046	0.264	-0.0245	0.2748	24.6445	-1.9535	35.3057

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 144:190)
2	X-RAY DIFFRACTION	2	(chain A and resid 191:321)
3	X-RAY DIFFRACTION	3	(chain A and resid 350:488)
4	X-RAY DIFFRACTION	4	(chain A and resid 495:533)
5	X-RAY DIFFRACTION	5	(chain A and resid 544:725)
6	X-RAY DIFFRACTION	6	(chain A and resid 726:836)
7	X-RAY DIFFRACTION	7	(chain A and resid 837:866)
8	X-RAY DIFFRACTION	8	(chain A and resid 867:881)
9	X-RAY DIFFRACTION	9	(chain A and resid 882:1090)

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi