PDB-7opz: Camel GSTM1-1 in complex with glutathione

ID or keywords:

Entry

Database: PDB / ID: 7opz

Title

Camel GSTM1-1 in complex with glutathione

Components

Glutathione transferase

Keywords

TRANSFERASE / Glutathione / Detoxification / Pesticides / Adaptation

Function / homology

Function and homology information

glutathione transferase / glutathione transferase activity / glutathione metabolic process / lipid metabolic process / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Camelus dromedarius (Arabian camel)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Papageorgiou, A.C. / Poudel, N.

Citation

Journal: Life / Year: 2022
Title: Structural and Functional Characterization of Camelus dromedarius Glutathione Transferase M1-1.
Authors: Perperopoulou, F. / Poudel, N. / Papageorgiou, A.C. / Ataya, F.S. / Labrou, N.E.

History

Deposition	Jun 2, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7opz.cif.gz	457.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7opz.ent.gz	315.7 KB	Display	PDB format
PDBx/mmJSON format	7opz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/op/7opz ftp://data.pdbj.org/pub/pdb/validation_reports/op/7opz	HTTPS FTP

-
Related structure data

Related structure data	7opyC 1gtuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7opz-2 6gsy-d 1xw6-2 5fwg-d 4gtu-1 1gtu-2 6gst-d 2f3m-2 7opy-2 6zjc-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#212 - Aug 2017 Glutathione Transferases similarity (11) #255 - Mar 2021 Cisplatin and DNA similarity (10)

Deposited unit

C: Glutathione transferase

A: Glutathione transferase

B: Glutathione transferase

D: Glutathione transferase

hetero molecules

104 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Glutathione transferase

A: Glutathione transferase

hetero molecules

defined by software
52.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutathione transferase

D: Glutathione transferase

hetero molecules

defined by software
52.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.832, 150.151, 191.785
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Glutathione transferase Mass: 25803.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: Cadr_000010866 / Production host: Escherichia coli (E. coli) / References: UniProt: G9B5E4, glutathione transferase
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.55 Å³/Da / Density % sol: 65.31 % / Description: Rod-like crystals
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: Tris-HCl 100mM, PEG 4000 24% (w/v), sodium formate 0.2 M

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2017 / Details: KB mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.55→95.9 Å / Num. obs: 49030 / % possible obs: 100 % / Redundancy: 6.6 % / B_iso Wilson estimate: 55.44 Å² / CC_1/2: 0.997 / R_pim(I) all: 0.099 / R_rim(I) all: 0.188 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.55→2.64 Å / Redundancy: 6.9 % / Num. unique obs: 4404 / CC_1/2: 0.348 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GTU

1gtu

Resolution: 2.55→95.89 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2735	2393	4.89 %
R_work	0.2056	46522	-
obs	0.2088	48915	99.94 %

Solvent computation

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

Displacement parameters

B_iso mean: 59.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→95.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7232	0	81	251	7564

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0079	7496
X-RAY DIFFRACTION	f_angle_d	0.9677	10076
X-RAY DIFFRACTION	f_chiral_restr	0.0478	1028
X-RAY DIFFRACTION	f_plane_restr	0.0064	1288
X-RAY DIFFRACTION	f_dihedral_angle_d	9.5621	996

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 (%)
2.55-2.6	0.3115	117	0.2842	2652	X-RAY DIFFRACTION	99.93
2.6-2.66	0.3327	130	0.288	2731	X-RAY DIFFRACTION	100
2.66-2.72	0.354	129	0.2791	2687	X-RAY DIFFRACTION	99.96
2.72-2.79	0.3503	155	0.271	2706	X-RAY DIFFRACTION	99.93
2.79-2.86	0.3006	127	0.2637	2693	X-RAY DIFFRACTION	99.93
2.86-2.95	0.3017	127	0.2545	2707	X-RAY DIFFRACTION	99.96
2.95-3.04	0.3639	150	0.2463	2700	X-RAY DIFFRACTION	99.96
3.04-3.15	0.3001	143	0.2294	2718	X-RAY DIFFRACTION	99.97
3.15-3.28	0.2749	168	0.2174	2669	X-RAY DIFFRACTION	99.89
3.28-3.43	0.3055	160	0.2108	2726	X-RAY DIFFRACTION	100
3.43-3.61	0.2854	157	0.1934	2716	X-RAY DIFFRACTION	100
3.61-3.83	0.2629	130	0.1809	2725	X-RAY DIFFRACTION	99.93
3.83-4.13	0.2174	156	0.1606	2729	X-RAY DIFFRACTION	100
4.13-4.55	0.2259	145	0.1472	2763	X-RAY DIFFRACTION	100
4.55-5.2	0.224	120	0.1566	2801	X-RAY DIFFRACTION	99.97
5.2-6.55	0.2411	143	0.2026	2818	X-RAY DIFFRACTION	99.97
6.56-95.89	0.3144	136	0.2496	2981	X-RAY DIFFRACTION	99.71

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	3.35333514301	0.901376407183	0.929581056588	1.50485737812	0.788497053781	3.48866088926	-0.0944479651625	0.245458216794	-0.170472391698	-0.255679393589	0.266461293268	-0.504693919763	0.0616506105241	0.585906002674	-0.133525536118	0.380696450284	-0.0302840187083	0.0860672268497	0.49956086848	-0.083744389732	0.532827614593	-5.99885546536	21.6245098053	-35.2292024244
2	3.2404869258	-0.729334866219	-1.11315778322	1.12781148529	1.323422337	1.5835328844	0.00744521001299	0.119555737592	0.41628151267	-0.233919333652	-0.00629136148478	0.0528724845721	-0.306488091502	0.0730991829371	0.00605929070421	0.353179732168	-0.0123837721256	-0.076944599085	0.362987613163	-0.01010406843	0.307247550028	-23.453197679	26.9555572086	-32.2273330239
3	2.81900025613	-0.431714601637	-0.254991169461	4.42398230133	-0.236503162446	3.74116208341	-0.277647874325	-0.157545886538	-0.275172272696	0.132863535521	0.352364491717	0.593982910875	0.438762823088	-0.743412544975	-0.0448719022735	0.382838326016	-0.112254579235	0.0111683173632	0.420859777293	-0.0746574592811	0.375714128312	-30.5544260864	14.2348663829	-33.3931277484
4	1.06353616149	-0.364508995655	-0.126466540543	3.69173219594	0.148915820438	2.97522470715	-0.040547197731	0.0380244309108	-0.0489745061277	-0.815872545452	-0.133698772348	0.299949659796	0.0459741699964	-0.564719538983	0.15703547232	0.367562099061	-0.0264618366067	-0.0237201304259	0.455846042308	-0.0783363338826	0.372501486193	-28.9834018751	15.9242177508	-41.5157471215
5	3.71546824192	-0.410851878679	0.866298434533	3.27687955311	0.440173245062	6.12581700205	0.206032403099	0.585602918407	-0.398130445695	-0.447018097328	-0.674092172011	-0.350881425481	0.525838356087	0.36815827407	0.351368781687	0.484145583452	-0.120583486901	0.0288425700965	0.473869723988	-0.0360043278531	0.482479085445	-16.2218807557	18.2815178212	-49.2959531066
6	6.46772278582	-0.612869056117	0.830540316176	6.26617829817	0.24120324327	2.90008601638	-0.147200471996	-0.249059277704	-0.51994068208	0.508219422669	-0.220021946371	-0.0472151595136	0.742134743287	0.193710640228	0.225187973014	0.86960177866	-0.0615291078519	-0.13914769707	0.630961179477	0.0702385089019	0.635914804565	-13.2206486839	4.84581507971	-34.1676275527
7	4.44849544745	0.625221125592	0.950868238341	1.54208252553	0.377264968677	2.93677189153	0.0626412982977	-0.534936367221	-0.213930318812	0.2870102513	-0.0311928882651	0.159291103619	0.348159498009	-0.4618281656	-0.027841873597	0.348927640009	0.00623226773735	0.0583667493849	0.411295991606	0.056116669789	0.359406929808	-34.6164058506	24.2016209066	-12.6200297467
8	4.28338437062	0.889000023233	-0.463417605699	4.0139401452	-0.656700614847	4.47507538349	0.0911265077649	0.143582012972	0.288278113129	0.0509893948384	0.0231032949428	0.275383824989	-0.814591974924	-0.239651543993	-0.122039735604	0.400448986573	0.0756045485092	-0.016668564413	0.436082314685	0.0180176091331	0.451579540759	-29.7707876146	35.2244022698	-21.9970906448
9	3.31295041303	2.19551203509	-1.49378180253	3.06306129034	-4.05331397387	7.05147019	-0.354411171941	-0.130844155549	-0.374769290501	-0.612224475718	0.105541145715	-0.730560090589	0.540833083407	-0.0375564897787	0.196479352777	0.439572183923	-0.0328181908657	-0.0181284453166	0.393082876346	-0.0385307692523	0.48537409909	-15.3275982735	26.2642981396	-20.3181138232
10	3.83750184799	0.531161265131	0.638999056802	3.64685582685	0.321956730161	4.36176622609	-0.188316151457	-0.0990450259835	-0.911853017469	-0.0592899991065	0.149442152837	-0.79444627638	0.95958336926	0.525447544022	0.0148586018065	0.537914026665	0.0902727037104	-0.0504198244175	0.535123961579	0.057629493843	0.529282665661	-7.68751526935	18.1636494632	-11.5844502588
11	3.77475413443	-0.213174112495	-4.7298986389	8.29865550865	1.15345478173	6.03681158721	0.189961706196	0.518373238472	0.655024062438	0.0414881701553	-0.559737721824	0.70976442371	-0.564589081416	-0.744125898501	0.373973391	0.438932460551	-0.0350206960306	-0.102700161787	0.353848122287	-0.0921466494371	0.475652339019	-11.0641477173	41.1238768591	-16.5054649579
12	2.01167588892	0.372281236517	-0.818716141728	3.54325873815	-0.716446061991	2.94745760156	-0.0162446127876	-0.353621631167	0.0554303017594	0.475477038718	-0.108226571903	-0.318599748825	-0.0431528963133	0.593007160638	0.103909048125	0.358422191299	0.0150934388679	-0.0265622830988	0.426889168642	-0.0590394488839	0.368784296983	-11.646702634	30.8568886695	-7.95065530201
13	1.48803620847	-0.177022472118	-0.566134926081	1.06985190744	0.220577663255	2.41567310931	0.148440973444	-0.180693133489	0.0368392732087	0.222820812601	0.0215930132325	0.0706282501412	-0.341117032226	0.603261823323	0.0347658172198	0.675848716107	-0.0328617272081	-0.027239647571	0.771948532565	-0.145319722764	0.676418922498	-24.8733780277	34.2520988673	-2.26721943947
14	7.69775922424	-0.888693374483	1.7489602658	3.0318227324	-0.583784190946	2.77843682327	0.362782911165	-0.905281118171	-0.371709324403	0.443383876725	-0.568280758615	-0.158358970111	1.49713523577	0.341379674861	0.0351900673454	0.810273318812	-0.00453957897842	0.000216152915366	0.771251654326	0.154948786557	0.702742913023	-23.5559054803	14.3454436759	-4.83933129113
15	4.99863777749	-1.40914330141	0.0781814844754	3.13825450472	0.116173855601	2.49646155809	-0.177309800306	-0.332882888303	0.0859739757257	0.908677382141	0.080351493082	-0.490197220662	0.57278781799	0.207395527245	0.092304711499	0.754196208842	0.0547754365023	-0.0777124137694	0.53859350406	-0.0425052782983	0.482002760411	-12.1385113471	-7.80821900214	-47.1222423787
16	1.17061801011	-0.95400806098	0.505564641219	4.24701827455	0.293369414988	1.9231253928	0.0809773721944	0.0584361828467	0.822612253554	1.19855352649	0.191216342014	-1.26481589954	-0.47327054438	0.856891640756	-0.0786276344458	0.772988363362	-0.16746956381	-0.103906829846	0.767707356033	-0.114586012773	0.986762051444	3.60955179658	2.59534350534	-51.6526793318
17	2.80792139775	-0.603319030771	0.887105510322	2.18777464326	0.138481931844	2.52769691007	-0.106195616749	0.259178682198	-0.556462879383	0.953596857867	0.413122160481	-0.536189161022	0.310558702402	0.626898168843	-0.290424480735	0.689315421689	0.124279606418	-0.178750718539	0.559736327532	-0.121979625234	0.643850023001	-2.85870615402	-14.1468581373	-54.5129229306
18	1.89020565865	-0.724313223933	0.556712410052	1.93865428387	1.58572583839	4.36522054351	-0.109623967763	0.158349782395	-0.216237799685	-0.093142493337	0.0310396662335	0.0591997275195	0.482336745159	-0.0136293718644	0.0660798885376	0.538163126836	-0.095506956358	0.057865390746	0.456301894983	-0.118126387965	0.467108044582	-20.5369356796	-8.84634494821	-61.1262887767
19	3.06855737691	1.75027673931	0.604739080227	4.07060128023	0.88775443368	3.65357028917	-0.121005398522	0.520010967193	0.276257500737	-0.46341352516	0.0828133180505	0.237332524346	-0.771100532233	0.0748862286251	0.0803363833616	0.709647625702	0.0771412252016	0.0161960210472	0.565717694579	-0.0349316515318	0.517177612077	-21.6590621363	10.3913062408	-65.1421861787
20	0.77835920026	-1.08306915447	-0.155251140448	1.61551088504	-0.335593046978	2.14468132661	0.127086745127	-0.163770730871	-0.130840391366	0.107205112966	-0.293752042303	0.48675730819	0.201432552134	-0.250397849845	0.188401192571	0.615579482058	-0.162994679981	0.0651293637416	0.543426858099	-0.106840127806	0.558701527959	-27.2954684137	-3.06042029919	-56.2760835514
21	4.47647053993	-0.602792094496	1.01411247411	5.21877806898	-0.908503659718	6.52928203719	0.00256721489022	0.519142338417	0.21226697798	-0.127109292825	0.0693792557759	0.273949036445	0.0601850072999	-1.38245943511	-0.237236594691	0.496040873451	-0.0462496200752	0.0641385180362	0.66503651348	-0.144803715971	0.498647318833	-31.2780580693	5.2962298929	-54.4337360296
22	2.77096709321	1.54191674265	-2.23567578622	2.28009008651	-0.144095154221	3.59973135763	0.18687584549	0.505107813918	-0.424675795684	1.06088077951	0.162355566852	-0.312446623217	-0.663563884201	-0.458045787363	-0.325619187724	0.752265192456	0.0626585566055	0.0387419659918	0.536430234201	-0.0179845221988	0.499146129472	-20.4297192815	-1.73571001501	-42.2330221534
23	2.64145992415	1.20061198796	0.00869837845461	4.88555541288	-0.275519577214	4.62581000829	0.195249262982	4.29873922164E-5	-0.13689057004	0.613389726033	-0.593473734057	0.0120683451396	-1.04570452825	0.279411591307	0.601997053438	0.696279527406	-0.137952794341	0.0174500029028	0.685181807266	-0.08587580721	0.712143825922	-7.85917313597	9.98984874503	-53.8372734615
24	3.35788679844	-3.13934973271	-1.04996128799	5.15897284243	-1.50683562775	2.96606698371	0.14211343305	0.662802939579	-0.0660482782056	-0.562195022309	-0.251973051411	0.274421928896	-0.28439287656	0.0269741402248	0.132311672423	0.541576992266	-0.0648062103384	-0.00179757506439	0.480379619559	-0.120349688863	0.412571883637	-19.7019662954	-12.1478343374	-84.3658349691
25	6.65563494993	2.04313112251	-1.87309144544	4.98631084276	-3.9101178716	4.74116218022	-0.308783554032	0.262722152011	1.51221502394	-1.09840397047	0.57747481584	-0.96708222771	-0.935368105275	0.501744376614	-0.419749150528	1.52175718318	-0.0850090263746	0.316392539862	0.954642639771	-0.0317176539058	1.2521442458	-15.4133461781	8.52756828138	-87.2124071021
26	2.61541300985	-1.58605922138	0.716747574822	3.16210186121	0.98080107592	4.38880631359	-0.112247668575	0.0825603168157	-0.0863770737442	0.102491746918	0.0977456574483	0.122549971029	0.00542049636422	-0.360786497809	0.0427167452748	0.437879608557	-0.065378242634	0.0547355944047	0.452191925255	-0.084122327538	0.368620759484	-19.310512068	-10.6202999316	-72.9054789358
27	3.23252193207	1.25369718396	0.402423063036	4.66382684438	0.212480860328	2.66133237325	-0.10423529056	0.113873391821	0.231535406542	-0.521536017615	0.246512053244	-1.06459236103	-0.585739665399	0.895619568267	-0.164085595112	0.709929460545	-0.132592867988	0.135998223332	0.837218687223	-0.227227006999	0.772208322264	3.47426889119	-5.39915451488	-72.6009470094
28	2.49389307754	-0.125819517954	0.595218196071	2.97632923725	-0.509681441487	3.75414286547	-0.0184504461967	0.0452292131633	-0.162085745657	-0.133960669368	0.298938047599	-0.968124541586	0.221302478006	0.7223226355	-0.222524059077	0.443963026499	0.0210101564073	0.052933311296	0.55307350506	-0.196170538457	0.62568933231	-2.47129244627	-19.6354177137	-76.120019156
29	4.90129061919	0.78845375693	0.0412022263796	6.53470067364	-3.3191004192	7.07558484814	0.036864903827	0.717369080094	-0.0834017621171	-0.0187423358716	-0.0791774585483	-0.303675674423	0.604214738695	-0.0816150056467	0.192045224943	0.614429685264	0.0725528072848	0.0693828307431	0.539995845381	-0.138305385288	0.47761711223	-11.0731847642	-23.4211274247	-88.1066231426
30	5.50559937918	2.83287678898	1.04506882554	6.90228737616	1.69353682681	4.98280188098	0.941059426981	-0.552660883655	1.37266358869	1.01740014664	-1.45390278345	0.0284831495855	-0.175500293865	0.26312861232	0.301704999269	0.782253400157	-0.134130962555	0.0840938661924	0.842216621617	-0.0581009391819	0.772639365272	-8.04547938356	-4.43686947628	-87.2564058079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 1 through 71 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 72 through 114 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 115 through 153 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 154 through 189 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 190 through 207 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 208 through 217 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 60 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 61 through 89 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 90 through 115 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 116 through 141 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 142 through 153 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 154 through 189 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 190 through 207 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 208 through 217 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 1 through 32 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 33 through 46 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 47 through 71 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 72 through 115 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 116 through 141 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 142 through 169 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 170 through 188 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 189 through 207 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 208 through 217 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 1 through 32 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 33 through 42 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 43 through 114 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 115 through 141 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 142 through 188 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 189 through 198 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 199 through 217 )

-
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