PDB-9qyi: Crystal structure of human S-adenosyl-L-homocysteine hydrolase co...

ID or keywords:

Entry

Database: PDB / ID: 9qyi

Title

Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / Protein dynamics / human SAHase / metal binding / AHCY

Function / homology

Function and homology information

Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / L-methionine cycle / Methylation / one-carbon metabolic process / melanosome / endoplasmic reticulum ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.59 Å

Authors

Malecki, P.H. / Imiolczyk, B. / Gawel, M. / Stepniewska, M. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of human S-adenosyl-L-homocysteine hydrolase complex with adenosine
Authors: Malecki, P.H. / Imiolczyk, B. / Gawel, M. / Stepniewska, M. / Brzezinski, K.

History

Deposition	Apr 18, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9qyi.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb9qyi.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	9qyi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/9qyi ftp://data.pdbj.org/pub/pdb/validation_reports/qy/9qyi	HTTPS FTP

-
Related structure data

Similar structure data	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	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

D: Adenosylhomocysteinase

E: Adenosylhomocysteinase

F: Adenosylhomocysteinase

G: Adenosylhomocysteinase

C: Adenosylhomocysteinase

H: Adenosylhomocysteinase

hetero molecules

389 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

D: Adenosylhomocysteinase

E: Adenosylhomocysteinase

hetero molecules

defined by author&software
Evidence: gel filtration
195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Adenosylhomocysteinase

G: Adenosylhomocysteinase

C: Adenosylhomocysteinase

H: Adenosylhomocysteinase

hetero molecules

defined by author&software
195 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.761, 90.195, 124.550
Angle α, β, γ (deg.)	96.235, 89.567, 105.531
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

-
Protein , 1 types, 8 molecules ABDEFGCH

#1: Protein	Adenosylhomocysteinase / AdoHcyase / S-adenosyl-L-homocysteine hydrolase Mass: 47640.777 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AHCY, SAHH / Production host: Escherichia coli (E. coli) / References: UniProt: P23526, adenosylhomocysteinase

-
Non-polymers , 6 types, 2743 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2713 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	N
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / Details: Morpheus D4

-
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: 0.915 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.915 Å / Relative weight: 1
Reflection	Resolution: 1.588→123.78 Å / Num. obs: 318137 / % possible obs: 90.43 % / Redundancy: 2.23 % / B_iso Wilson estimate: 16.88 Å² / CC_1/2: 0.997 / Net I/σ(I): 7.7
Reflection shell	Resolution: 1.588→1.709 Å / Num. unique obs: 15905 / CC_1/2: 0.517

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419+SVN	refinement
XDS		data reduction
XDS		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.59→123.78 Å / SU ML: 0.1854 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.808
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2136	1629	0.51 %
R_work	0.1768	316401	-
obs	0.177	318030	69.11 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 25.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→123.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26640	0	541	2713	29894

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	27885
X-RAY DIFFRACTION	f_angle_d	0.8541	37863
X-RAY DIFFRACTION	f_chiral_restr	0.0551	4264
X-RAY DIFFRACTION	f_plane_restr	0.0067	5089
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4231	10387

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 (%)
1.59-1.63	0.2728	12	0.3383	2400	X-RAY DIFFRACTION	6.28
1.63-1.69	0.3084	38	0.3025	8574	X-RAY DIFFRACTION	22.53
1.69-1.75	0.3226	94	0.2831	14326	X-RAY DIFFRACTION	37.6
1.75-1.82	0.3102	104	0.2661	19316	X-RAY DIFFRACTION	50.63
1.82-1.9	0.2584	114	0.2438	24142	X-RAY DIFFRACTION	63.2
1.9-2	0.2635	146	0.237	29280	X-RAY DIFFRACTION	76.68
2-2.13	0.2553	181	0.2207	34186	X-RAY DIFFRACTION	89.81
2.13-2.29	0.2452	176	0.1971	36764	X-RAY DIFFRACTION	96.36
2.29-2.52	0.2209	201	0.186	36773	X-RAY DIFFRACTION	96.39
2.52-2.89	0.2197	175	0.1761	36828	X-RAY DIFFRACTION	96.48
2.89-3.64	0.1957	188	0.1512	37031	X-RAY DIFFRACTION	97.05
3.64-123.78	0.1641	200	0.1317	36781	X-RAY DIFFRACTION	96.42

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	2.63265155443	0.783593721349	-0.260134704736	1.56877945805	0.111308328678	0.911715925901	-0.11236365839	0.248186051694	-0.133816517016	-0.34250831213	0.127283066882	-0.368532237833	-0.0875880081313	0.28334793912	-0.0111765490625	0.234399890369	0.00222105692884	0.118934659799	0.354516257849	0.0590308545209	0.201969621231	25.7341615061	18.9827721063	-53.0371991507
2	2.10985342675	1.3104146033	0.0187858377369	4.63307043825	-1.13632762802	2.78999932134	-0.0257931793438	0.25887024249	0.293815938919	-0.188667509549	0.0443682324963	0.242436911545	-0.21050008097	-0.153880411845	-0.0306197087407	0.13508593744	0.00210555043784	0.08675512905	0.224127661653	0.0650858407223	0.127952021237	13.4375955187	30.2447833851	-50.2696538436
3	1.28113285364	-0.178854894784	-0.363083821439	0.852795752766	0.171154863383	0.683267841926	0.0407572146171	-0.0509044658196	0.193834445641	-0.0463507167166	-0.0821625109576	-0.319673365064	-0.208456287456	0.346785808293	0.00521131601123	0.178258619195	-0.110648059073	0.0707991282241	0.34623057153	0.0859783896123	0.262727669637	26.124990013	30.0613086297	-42.5003612525
4	1.09110976705	-0.109113173083	0.0996140669555	2.50278876647	-0.409271192192	0.337938583835	0.0284107564683	-0.0757523322777	0.231536556895	0.177377974693	-0.0385215719265	-0.0438728019157	-0.156481367578	0.247497062459	0.00914621151166	0.16198527592	-0.0736751622796	0.0328972790475	0.175936322561	0.00136885482919	0.109823129808	13.8792733952	24.2079322556	-31.4935547589
5	1.52026155208	-0.498175789536	-0.323166258036	2.40235592847	0.274465072026	0.601996496535	0.00456967423959	-0.0308493267662	0.0360065666211	0.0995462262074	-0.0345152848446	-0.0679933363734	-0.0584047649538	0.222638853496	0.0320324618312	0.0782995059313	-0.0270246853679	0.00141087348832	0.120012274514	0.000965731881262	0.0410833937892	12.379966778	8.78081697121	-20.5304991224
6	0.877499894125	-0.345751822914	0.707646102973	0.540913154293	-0.326514838748	0.892337912242	-0.0241729804769	-0.0937140884071	0.130976660145	0.0296993012341	-0.0735561320964	-0.261062479465	-0.0249065285674	0.42627046022	0.0907087263809	0.104057964144	-0.0236442647865	7.84073692603E-5	0.403361067742	0.0266721965769	0.182993922878	28.8252825301	8.19654443446	-24.3511840341
7	1.86162837011	0.799009037369	-0.61059879269	0.435699916799	-0.387231656126	1.47664354606	0.00192754340552	0.112152512152	0.328140217682	-0.100575177806	0.0278514512532	0.0456227002977	-0.285740606043	0.017344265494	-0.026647681135	0.159386126386	-0.0238791840648	0.021692281282	0.116916535573	0.0416529148699	0.161971199384	7.17216840529	32.4958137099	-41.1525629421
8	1.15360034628	-0.160926508567	0.246728360018	1.17512146535	0.262417998105	1.13760082307	0.0225206012693	0.104808198787	0.250771220312	-0.0723486234536	0.0483331770246	0.184301016417	-0.356574476246	-0.101926137728	-0.0479715253226	0.1853224695	0.00689737092011	0.0385751801163	0.0666514863752	0.0554590680514	0.175588420854	-10.8645192151	26.1383580084	-39.0355445329
9	0.847236875458	-0.405717657951	-0.0813808085927	0.890567210436	-0.00931155688666	0.489514642831	-0.0248183239406	-0.141166177799	0.122039716007	0.183875439967	0.135906221665	0.173981595396	-0.231043215236	-0.13097617792	-0.0878367010837	0.249845313228	0.0912568270684	0.120089396155	0.164436364185	0.0334313197553	0.214169176786	-22.6771815455	24.7264588586	-8.13695637352
10	0.465950639177	-0.174220695344	-0.0563529769788	0.49976548216	-0.177398243538	0.684536706809	0.0206186215965	-0.01992273259	0.0720092767383	0.0493361833443	0.0888823757264	0.130373625914	-0.147908026483	-0.0741266333192	-0.080910504963	0.104378876726	0.0045532915364	0.0379667397824	0.0556808362871	0.0335411196824	0.127111779926	-12.7935812651	16.4691315634	-25.5479477371
11	0.435813477973	-0.194403054259	-0.161323522316	0.304798503822	0.0701909744805	0.0901499890849	0.0508649651058	0.186167161255	-0.186057661374	-0.217726117865	-0.0832924317001	-0.134423203745	0.392660057941	0.372386090996	0.068220952858	0.361358567105	0.486888090926	0.164321915276	0.5143923359	-0.0533705236781	0.160626127684	24.5597172213	-19.6504002166	-42.1730263451
12	1.6463864022	0.841376342275	-0.455865303761	1.64390112262	0.339012808248	0.58603094889	0.0462275410253	0.146091674009	-0.0431324687307	-0.15236931467	-0.0214497472798	0.0879879305901	0.188649130797	0.0876857407254	-0.0203633134271	0.167975104558	0.0359925937389	-0.0397701035541	0.102159140344	-0.0284976596964	0.0690220149222	-0.567492595592	-3.54926794334	-44.716110704
13	0.798373397289	0.116783640945	0.516567987432	0.276815971749	0.0258971655579	1.7931476773	0.00535330876593	0.267223002985	-0.0715913024292	-0.237368460289	-0.00513928384138	-0.0575987054371	0.211965714213	0.236723226658	0.00667085527848	0.272818939123	0.117698403604	0.0362521192362	0.300505891332	-0.0273714315483	0.102615081509	10.7902348323	-1.16800669933	-56.7156914033
14	1.36330494151	0.221584025821	-0.367624486682	0.679036532149	0.042638440697	0.371400784643	0.0156660094742	0.0722442798936	-0.36229001193	-0.110585675187	-0.0530197585499	0.00219117266456	0.386267281532	0.234593448591	0.0590998633598	0.353244681635	0.192417306293	-0.0207105554795	0.167742264646	-0.00610016269488	0.220746234564	11.7948807092	-24.5607834163	-24.3664916711
15	2.75125355595	-0.00389143379956	-1.27297867375	0.622698720097	0.995899420175	2.76014160735	0.0367664271324	-0.19178544615	0.07809357689	0.0910148469866	0.0822611428199	0.403523357957	0.248229045296	-0.30563219816	-0.103799762305	0.171817811647	-0.105123161101	-0.0310127115413	0.258940193021	0.133023075298	0.415666234619	-35.2762483532	-12.1078775713	-21.5570058699
16	0.819376605646	0.794759860994	-0.0377226100976	1.74127470069	0.429205772184	0.752509821495	-0.183996888572	0.193342125602	-0.0603834647685	-0.328586451525	0.0355309130116	0.381349377389	0.227627307396	-0.255514263478	0.181927550658	0.316372986172	-0.153054709484	-0.128008524466	0.187348102307	0.0405597855988	0.456905174263	-28.0821214918	-22.5906298995	-32.6561150911
17	0.490603960727	0.34139549534	-0.531348290498	1.00177765514	-0.283451697144	1.04771404939	0.0356953345061	-0.0787647475776	-0.19696483894	0.0362368074033	0.0240680892155	0.126572926879	0.238500956041	-0.171531105166	0.00576625164488	0.213672302503	-0.133641654849	-0.0583648461927	0.222062954809	0.191677553771	0.466148473322	-30.5593381045	-21.4996653103	-18.0042098969
18	0.571854948084	0.56816130348	-0.499325973151	2.26927078472	-0.349972024897	1.1149861688	-0.039073705335	-0.080118099469	-0.154355432147	0.208064953671	-0.0786417267865	0.118815592879	0.235719215634	-0.0848070544526	0.134754254295	0.37278231854	-0.119982733498	-0.0943031674285	0.176467610599	0.124989647885	0.512801993307	-21.5646053002	-32.6920351479	-18.3099278019
19	0.324846413497	0.0732938497151	-0.260916939169	1.4356071663	0.054964409338	0.216926455397	-0.0303329402307	-0.0277198400073	-0.219971477654	0.0140840988578	0.109895412307	0.0224891745895	0.302696877847	-0.0342592798733	-0.0324838693855	0.261119817584	-0.0247675106053	-0.0604918687251	0.0840616446195	0.0258474193326	0.290369859945	-11.4797259005	-20.2703333996	-22.293704881
20	1.55626936844	-1.68242692138	-0.199338099186	4.24897746975	0.955926522128	1.63943463579	0.0854929589813	0.0975458173021	0.0666054364135	-0.270589450994	0.0228216861592	0.0263094348278	-0.174585489198	-0.0400668194267	-0.0994534271799	0.076403452333	-0.0118206205009	0.0180730995575	0.0461168615659	0.00857385225526	0.0874480554711	-3.82901638522	-2.93093234143	-18.4216267465
21	1.69812822269	-0.287625064227	-0.858093287591	2.22714200297	-0.23483654889	1.06122629361	0.0106023568141	-0.105514599697	-0.117995192477	0.0501958141173	0.0086953967489	-0.0438911310168	0.130402975422	0.120052854279	-0.0177908754729	0.0982013713952	0.0260898579193	-0.0253612992169	0.0560892166062	0.00493160153605	0.0734760604002	3.07082661407	-9.49649347012	-13.8017403088
22	1.3592501666	0.198580349701	0.35410681389	0.899093739383	-0.282229036909	1.80518641985	0.0056354643022	-0.280909297281	-0.18975436835	0.132277508663	0.124179831784	0.216214071414	0.143758004415	-0.17494783584	-0.109929422124	0.137237327037	0.0162855406	0.0349641400298	0.120260764874	0.0642426971165	0.16699504229	-10.7818745574	-7.36336629962	-3.10506594969
23	0.271576136685	-0.164805682419	-0.260266224182	0.175360810335	0.148198533107	0.249087449007	-0.0558004517461	0.101741565759	-0.281197195438	-0.183738563833	0.137288095943	-0.000658443878768	0.317563269669	-0.0851221495866	-0.0191691168072	0.386881170511	-0.115045627301	-0.123619870757	0.121310123873	0.00898506776668	0.360971740527	-17.3896172742	-25.8615981597	-34.1673925365
24	0.845572500381	-0.264522475877	-0.274338702766	0.695746765893	0.423001649357	0.830670329011	0.0340008830802	0.318411148473	-0.240339208843	-0.332388354904	-0.0410737726619	0.128247244998	0.205845801764	0.0456431242274	0.0209376639842	0.399098821207	0.0262381642457	-0.0959653019614	0.167601449457	-0.0882989510254	0.230862650986	-5.49527905813	-18.0445665112	-47.6569865544
25	4.55855762948	1.34355634686	0.0949734769394	1.42757458495	-0.298896901974	1.476587254	-0.174522569214	0.472245284107	0.123555927571	-0.293136773573	0.248767695573	0.340111906885	0.0889848973293	-0.035558293572	-0.070932474614	0.222604373458	-0.0142589578826	-0.110999411958	0.203328691579	0.0222419707632	0.20254725867	14.6299519705	7.64452636101	-117.137856717
26	1.50771864587	0.959543454297	-0.619137571797	4.75240212055	2.03205040044	3.60557528795	0.157370699287	0.304051136942	-0.363189524997	-0.385204974507	0.0350864923833	-0.262529967308	0.283168159927	0.332225739296	-0.18945108954	0.256296339713	0.123109074648	-0.136023471197	0.284148468534	-0.0252077791129	0.1709239566	27.0306548941	-3.65669764925	-116.885429816
27	2.45341881312	0.339829290203	-0.308440208417	1.61028540472	0.122473793276	1.00468884916	0.156369523241	0.115222348647	-0.241904251981	-0.160898976737	0.0183476851568	0.276026909034	0.378542770011	-0.117722058664	-0.158905527893	0.24905452719	-0.0181638651366	-0.153535722396	0.172655645004	0.0316135416323	0.237632645778	13.2347871039	-1.8702670635	-111.547254488
28	1.14246814403	-0.0426719507595	-0.0604421137406	1.38691795182	0.276841850694	0.851003032948	0.154981759281	-0.140386563622	-0.384641184688	0.039641860305	-0.00253310181578	0.111857386123	0.375059159031	0.0503594001717	-0.142850603432	0.28290593116	0.0087038752833	-0.119359572806	0.198508281325	0.0404172214706	0.219618562014	23.0133631978	-6.58976191126	-99.9459903948
29	1.05355296705	-1.02930179404	0.70465603576	2.50455390739	-0.372275787872	0.539301276666	0.0440072522016	-0.0589653025149	-0.0535505387131	0.115990537932	0.00408928873817	0.0979784407645	0.0133522978789	-0.0818459119754	-0.0382502930665	0.0964066409893	-0.0223431352017	0.00942154160723	0.21610414562	0.0304688429999	0.0774013464304	27.8854035591	10.2426175045	-82.8109480362
30	2.08367836115	-0.0941731170379	-1.03787095366	1.43378978386	0.16607918515	1.91009441413	0.00461289573135	-0.0750221713346	-0.151314423889	0.14220322987	0.109576592912	0.444376110874	0.0363882410892	-0.417556814423	-0.0830218615595	0.120539260533	-0.00998092261167	0.0202866825483	0.27145186319	0.0770379038746	0.217063209783	11.5953724026	11.8528911167	-86.5691974614
31	2.03951018929	0.061721620566	0.625280266578	0.285083302629	-0.191822917675	0.628799018388	0.178281919313	0.0995218743078	-0.438139290508	-0.115657160898	0.0128094731224	-0.0888456190769	0.315999422523	0.261955958269	-0.163237227307	0.270654622545	0.121418055254	-0.0659278111996	0.298065409004	-0.0512108848616	0.195093492505	41.4001982469	-5.35839784676	-107.0138446
32	2.0232738477	-0.0889505554718	0.394425611233	2.54258716638	0.087983731522	1.29500137666	0.0128211023073	0.101051203784	0.31970081443	-0.0462737111348	0.0351550743419	0.29159475582	-0.338335891463	-0.331291101976	-0.0295705167374	0.168256543256	0.0828344872307	0.0237305203444	0.253059719517	0.0386530576484	0.21839585581	10.1983935082	41.9893078035	-97.9155172018
33	1.56376335982	-0.294588734323	0.375304430651	0.94026698738	0.775724781023	1.14042452787	-0.0239284367845	0.164233234599	0.481013096323	-0.23818101554	0.0311395074688	-0.18096507987	-0.396472143864	0.0185135572541	-0.00436661061318	0.234732686713	-0.0103444744464	0.0432346997939	0.237332713194	0.0831843178845	0.219550695633	25.9967574597	44.6819172496	-97.7230945519
34	1.2134079687	1.04577780554	0.576926606331	2.80125403511	0.484230232601	0.282149776306	0.0741196429843	0.110395928533	0.00567285481793	-0.0302493624219	-0.0975639992143	-0.0964082879376	-0.0250392264593	0.0803080999436	0.0239894028051	0.0933861386765	-0.0166772595766	0.0107187711825	0.2299982342	0.0296534514447	0.0733431353304	40.7172714054	28.3172470881	-104.000755764
35	0.945008736654	0.407073600938	-1.03786845953	0.639904729362	0.162807092686	3.69640995616	0.0242605633358	0.304143630099	0.1081148255	-0.139462131382	0.0206254727291	0.0853489432975	-0.187479747338	-0.101120414048	-0.0417134941782	0.123166155266	0.0183686391968	-0.0183175393725	0.247230886361	0.0421535865341	0.107715651571	29.0605822258	28.3806628819	-116.079224303
36	4.66848879917	0.854355012368	0.131437186257	0.473409286683	-0.974994769361	4.19580806653	-0.0664141673761	-0.162120003064	0.895985480169	0.421205581538	-0.0252706630475	0.168553474952	-0.898458095951	-0.0933303688299	0.0692094463177	0.32309379328	0.0453098633238	0.00437444186076	0.212103073328	-0.0232205797908	0.280199926295	22.6004753016	47.2646743924	-85.3741905872
37	2.53200788062	0.493451001817	1.10496201617	1.48367960471	0.331259297585	4.31677841929	0.0567841399253	-0.438077730429	0.396608834941	0.368491151453	-0.0806189990715	0.149556158501	-0.568001290089	-0.107007992044	0.0295227922617	0.249275579763	0.0418056257989	0.0193265258532	0.184047368704	-0.0380756224202	0.159804004129	34.9803630329	39.5804065633	-71.8699712108
38	1.74741652609	-0.243401709599	0.395125882148	1.52041153407	-0.0210280416238	1.10813006285	0.114140117618	-0.0138799287979	-0.29537720978	0.187803856825	-0.00287862886137	-0.236679917968	0.327801611947	0.240957910844	-0.0996883442323	0.263120518591	0.0807731416927	-0.102825790353	0.281141753629	0.00128494215182	0.21466777673	64.1579115229	-6.73056125904	-73.0956959897
39	0.753574353823	0.860297937403	0.00203459124641	2.37570991062	-0.758075975353	1.13549507318	0.0771028229503	0.105976897491	-0.112170264838	-0.0656016802425	0.00411595646093	-0.0712723039195	0.190621846028	0.148398183947	-0.0812352055503	0.120771099129	0.0360663745772	-0.0357977782126	0.279860726175	-0.0177752079197	0.110804227329	53.642933716	3.06810168938	-89.186889795
40	1.09287969976	0.219565249415	-0.458933480936	0.683231683562	0.132839251708	0.378557711957	0.0510284871124	0.189455839492	-0.0241332679573	-0.0795385021104	0.00561434572566	-0.20524299363	0.0174896866777	0.29520072118	-0.0433531789338	0.12702986876	0.0322609742681	0.0167685460373	0.386523656251	0.000405836617362	0.140936237748	62.8244350166	11.9968543573	-97.7756552061
41	2.97815024472	-0.332324563719	0.661823516867	0.24444604	0.280779953956	1.81802498774	0.12458416814	-0.132789282613	-0.593398623767	0.0554068573525	0.109798985667	0.13349988437	0.39087546307	-0.00887672542032	-0.211732222929	0.255381481397	-0.0317486796292	-0.0696141836142	0.189526008126	0.0663624815516	0.21763089429	39.6818380007	-8.36003230032	-78.5191960918
42	2.29214118573	0.176940356098	-0.399256956003	2.23884943839	0.264131058505	0.792213358196	-0.0818303519086	-0.125934316353	0.429440003658	0.153432076318	0.0348503487118	-0.375926968732	-0.410380199759	0.490650672571	0.0210640943082	0.307368829374	-0.158316065417	-0.0908183523163	0.39070855729	0.0202798152583	0.355569490601	69.9166038449	40.5093733779	-77.8586988568
43	1.79165344385	0.0773365229707	-0.248605724683	1.2745007419	-0.311905558115	1.11973689513	-0.063621590088	-0.106722016039	0.508581302101	0.155474917633	0.0768867126873	-0.191139971795	-0.472825750469	0.164154001343	-0.026645603139	0.299637553962	-0.0916429033024	-0.046068776122	0.26418051076	-0.0419437934179	0.26551165111	54.0539487322	42.7947598287	-77.3903709801
44	1.5268179989	-1.27518021008	0.632686967003	2.80908743156	-0.141581574828	0.35636073529	0.0454024341103	-0.0798698688419	-0.0331321566916	0.0853926894644	-0.0313733220891	0.0256998532462	-0.038464365189	0.0257262680615	-0.00900083942193	0.11022699927	-0.0297694687277	0.0155512285016	0.200392599994	0.00714174781397	0.0619998351735	39.9086721149	25.163494335	-74.3218185001
45	1.33933776647	-0.384835064725	-0.440123182815	0.995369841875	-0.701277708263	4.0496297779	-0.0242878787154	-0.282589450998	0.0827099115652	0.208054481454	0.0182360560891	-0.108279887294	-0.240397696225	0.245921495255	0.00980395207087	0.156087611844	-0.028615905346	-0.0310715629632	0.219575419126	-0.0136434515	0.104036474366	51.4966349439	22.8311233333	-62.6019061195
46	2.5704631651	-0.109021744464	0.163797579539	0.242775758044	0.0370334872293	1.10269279431	-0.126689728524	0.0898863998634	0.467075727427	-0.0313614587946	-0.029521648348	-0.139739819029	-0.503730899897	0.309151502051	0.137833827629	0.320886550182	-0.118054207368	-0.0256503277556	0.227690483524	0.0633950111207	0.266808263952	51.9008316889	45.6551289445	-95.389045734

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 28 )	A	A	3 - 28	1 - 26
2	2	chain 'A' and (resid 29 through 57 )	A	A	29 - 57	27 - 55
3	3	chain 'A' and (resid 58 through 157 )	A	A	58 - 157	56 - 155
4	4	chain 'A' and (resid 158 through 207 )	A	A	158 - 207	156 - 205
5	5	chain 'A' and (resid 208 through 283 )	A	A	208 - 283	206 - 281
6	6	chain 'A' and (resid 284 through 354 )	A	A	284 - 354	282 - 352
7	7	chain 'A' and (resid 355 through 398 )	A	A	355 - 398	353 - 396
8	8	chain 'A' and (resid 399 through 432 )	A	A	399 - 432	397 - 430
9	9	chain 'B' and (resid 3 through 169 )	B	D	3 - 169	1 - 167
10	10	chain 'B' and (resid 170 through 432 )	B	D	170 - 432	168 - 430
11	11	chain 'D' and (resid 3 through 207 )	D	G	3 - 207	1 - 205
12	12	chain 'D' and (resid 208 through 283 )	D	G	208 - 283	206 - 281
13	13	chain 'D' and (resid 284 through 354 )	D	G	284 - 354	282 - 352
14	14	chain 'D' and (resid 355 through 432 )	D	G	355 - 432	353 - 430
15	15	chain 'E' and (resid 3 through 28 )	E	J	3 - 28	1 - 26
16	16	chain 'E' and (resid 29 through 57 )	E	J	29 - 57	27 - 55
17	17	chain 'E' and (resid 58 through 126 )	E	J	58 - 126	56 - 124
18	18	chain 'E' and (resid 127 through 157 )	E	J	127 - 157	125 - 155
19	19	chain 'E' and (resid 158 through 207 )	E	J	158 - 207	156 - 205
20	20	chain 'E' and (resid 208 through 235 )	E	J	208 - 235	206 - 233
21	21	chain 'E' and (resid 236 through 283 )	E	J	236 - 283	234 - 281
22	22	chain 'E' and (resid 284 through 354 )	E	J	284 - 354	282 - 352
23	23	chain 'E' and (resid 355 through 398 )	E	J	355 - 398	353 - 396
24	24	chain 'E' and (resid 399 through 432 )	E	J	399 - 432	397 - 430
25	25	chain 'F' and (resid 3 through 28 )	F	M	3 - 28	1 - 26
26	26	chain 'F' and (resid 29 through 57 )	F	M	29 - 57	27 - 55
27	27	chain 'F' and (resid 58 through 126 )	F	M	58 - 126	56 - 124
28	28	chain 'F' and (resid 127 through 207 )	F	M	127 - 207	125 - 205
29	29	chain 'F' and (resid 208 through 283 )	F	M	208 - 283	206 - 281
30	30	chain 'F' and (resid 284 through 354 )	F	M	284 - 354	282 - 352
31	31	chain 'F' and (resid 355 through 432 )	F	M	355 - 432	353 - 430
32	32	chain 'G' and (resid 3 through 142 )	G	P	3 - 142	1 - 140
33	33	chain 'G' and (resid 143 through 207 )	G	P	143 - 207	141 - 205
34	34	chain 'G' and (resid 208 through 283 )	G	P	208 - 283	206 - 281
35	35	chain 'G' and (resid 284 through 354 )	G	P	284 - 354	282 - 352
36	36	chain 'G' and (resid 355 through 398 )	G	P	355 - 398	353 - 396
37	37	chain 'G' and (resid 399 through 432 )	G	P	399 - 432	397 - 430
38	38	chain 'C' and (resid 3 through 157 )	C	C	3 - 157	1 - 155
39	39	chain 'C' and (resid 158 through 235 )	C	C	158 - 235	156 - 233
40	40	chain 'C' and (resid 236 through 354 )	C	C	236 - 354	234 - 352
41	41	chain 'C' and (resid 355 through 432 )	C	C	355 - 432	353 - 430
42	42	chain 'H' and (resid 3 through 142 )	H	H	3 - 142	1 - 140
43	43	chain 'H' and (resid 143 through 207 )	H	H	143 - 207	141 - 205
44	44	chain 'H' and (resid 208 through 283 )	H	H	208 - 283	206 - 281
45	45	chain 'H' and (resid 284 through 354 )	H	H	284 - 354	282 - 352
46	46	chain 'H' and (resid 355 through 432 )	H	H	355 - 432	353 - 430

-
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

-
Protein , 1 types, 8 molecules ABDEFGCH

-
Non-polymers , 6 types, 2743 molecules

-
Details

-
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

-Protein , 1 types, 8 molecules ABDEFGCH

-Non-polymers , 6 types, 2743 molecules

-Details

-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

-
Protein , 1 types, 8 molecules ABDEFGCH

-
Non-polymers , 6 types, 2743 molecules

-
Details

-
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