PDB-6apv: Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase...

ID or keywords:

Entry

Database: PDB / ID: 6apv

Title

Trypanosoma brucei hypoxanthine guanine phosphoribosyltransferase in complex with [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE /

Trypanosoma brucei / Purine salvage / acyclic nucleoside biphosphonate

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity /

hypoxanthine phosphoribosyltransferase activity / IMP salvage /

glycosome / nuclear lumen / ciliary plasm / purine ribonucleoside salvage /

nucleotide binding /

metal ion binding ...
Similarity search - Function

Biological species

Trypanosoma brucei brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.993 Å

Authors

Teran, D. / Guddat, L.W.

Citation

Journal: PLoS Negl Trop Dis / Year: 2018
Title: Evaluation of the Trypanosoma brucei 6-oxopurine salvage pathway as a potential target for drug discovery.
Authors: Dolezelova, E. / Teran, D. / Gahura, O. / Kotrbova, Z. / Prochazkova, M. / Keough, D. / Spacek, P. / Hockova, D. / Guddat, L. / Zikova, A.

History

Deposition	Aug 18, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6apv.cif.gz	320.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6apv.ent.gz	261.9 KB	Display	PDB format
PDBx/mmJSON format	6apv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/6apv ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6apv	HTTPS FTP

-
Related structure data

Related structure data	6apsC 6aptC 6apuC 6aqoC 6ar9C 5jsqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6apu-d 3o04-d 3a50-3 6jl2-3 6hqg-1 5qk9-2 4pjt-3 5kpn-1 3i8p-d 1z5v-d 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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (6)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

defined by author&software
Evidence: SAXS
49.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.480, 94.555, 109.692
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁22₁

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / / HGPRTase Mass: 24221.775 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: HGPRT / Production host: Escherichia coli (E. coli) References: UniProt: Q07010, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-3L4 / [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid Mass: 438.270 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₂₀N₆O₈P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.39 Å³/Da / Density % sol: 48.64 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2 M lithium sulfate and 0.1 M Bis-Tris

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 1.99→47.44 Å / Num. obs: 64145 / % possible obs: 99 % / Redundancy: 9.4 % / R_pim(I) all: 0.061 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.99→2.84 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3961 / R_pim(I) all: 0.24 / % possible all: 84.3

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5JSQ

5jsq

Resolution: 1.993→47.278 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1981	2005	3.14 %
R_work	0.1636	-	-
obs	0.1647	63913	99.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.993→47.278 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5599	0	148	574	6321

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6049
X-RAY DIFFRACTION	f_angle_d	0.998	8246
X-RAY DIFFRACTION	f_dihedral_angle_d	12.079	4957
X-RAY DIFFRACTION	f_chiral_restr	0.064	947
X-RAY DIFFRACTION	f_plane_restr	0.007	1040

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 (%)
1.9929-2.0428	0.2414	146	0.1854	4211	X-RAY DIFFRACTION	96
2.0428-2.098	0.209	138	0.173	4379	X-RAY DIFFRACTION	100
2.098-2.1597	0.1963	140	0.1556	4369	X-RAY DIFFRACTION	100
2.1597-2.2294	0.1748	141	0.1631	4410	X-RAY DIFFRACTION	100
2.2294-2.3091	0.251	133	0.1901	4371	X-RAY DIFFRACTION	100
2.3091-2.4016	0.2177	154	0.1557	4412	X-RAY DIFFRACTION	100
2.4016-2.5108	0.2015	147	0.1571	4389	X-RAY DIFFRACTION	100
2.5108-2.6432	0.2194	144	0.1587	4413	X-RAY DIFFRACTION	100
2.6432-2.8088	0.1879	142	0.1636	4428	X-RAY DIFFRACTION	100
2.8088-3.0256	0.2106	139	0.1622	4447	X-RAY DIFFRACTION	100
3.0256-3.33	0.1905	141	0.1595	4471	X-RAY DIFFRACTION	100
3.33-3.8117	0.201	145	0.1603	4475	X-RAY DIFFRACTION	100
3.8117-4.8016	0.1523	149	0.1406	4497	X-RAY DIFFRACTION	100
4.8016-47.2908	0.2091	146	0.1888	4636	X-RAY DIFFRACTION	98

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	1.2622	-0.5401	-0.7898	2.3958	0.6975	3.2356	-0.0327	0.0776	-0.0014	-0.0563	0.0486	0.0728	-0.0481	-0.0759	-0.0006	0.08	-0.0164	-0.0181	0.0816	0.0131	0.0955	17.3154	99.7917	-91.448
2	0.8638	0.6239	0.472	7.5247	2.866	2.4941	-0.1798	-0.7767	-0.0389	0.5679	0.1399	-1.1911	0.6255	1.2442	-0.109	0.2897	0.0078	0.0559	0.4771	-0.0674	0.3814	33.815	96.5224	-100.5601
3	1.2632	0.3147	-0.1139	2.1082	-0.2798	1.7816	-0.0241	-0.0569	0.1069	0.1733	0.0516	-0.2413	-0.202	0.2004	-0.0277	0.094	-0.0018	-0.0345	0.1	-0.0184	0.1378	24.3234	109.2414	-83.2516
4	4.5507	1.8952	-2.7341	6.4632	1.2855	8.099	-0.0798	0.4389	0.009	-0.7602	0.1232	0.0738	0.2055	-0.7383	-0.0626	0.1861	-0.0229	-0.064	0.1534	-0.0077	0.1964	10.3164	79.2443	-94.7306
5	1.5203	0.7728	0.438	2.3045	0.546	3.3344	-0.0144	-0.0833	-0.0577	0.2248	0.0132	0.0976	-0.015	-0.1309	-0.01	0.1079	0.0324	-0	0.0778	0.0221	0.1156	17.3744	90.1473	-72.2882
6	6.6672	0.7737	-1.9933	4.6027	0.3627	5.2159	0.1388	-0.0687	0.2728	0.0944	0.0244	-0.6241	-0.0567	0.6573	-0.1303	0.0916	0.0303	-0.0393	0.142	0.0171	0.1022	26.1239	92.7051	-75.3151
7	0.9638	0.3162	0.5584	3.6522	2.585	5.6006	0.0091	0.0513	0.0259	-0.2353	0.2771	-0.5825	-0.4984	0.3759	-0.2433	0.1079	-0.0143	0.0007	0.1768	0.0046	0.1667	28.0721	84.849	-74.5281
8	1.6204	2.8078	2.1556	5.7676	3.9688	4.1139	-0.0723	-0.2531	-0.0204	0.5527	0.276	-1.0623	0.2302	0.9006	-0.1806	0.204	0.047	-0.0943	0.2362	-0.0093	0.3915	34.65	81.1788	-73.1809
9	1.2617	-0.1695	0.1193	1.9424	-0.0793	2.5061	-0.0284	-0.0343	-0.1659	0.0392	0.0805	-0.1183	0.1902	0.0846	-0.0549	0.0539	0.0104	-0.0042	0.0868	-0.0162	0.1446	21.2658	79.2147	-83.3692
10	3.3183	-2.2734	-1.3216	1.7873	-0.0521	4.4378	-0.1416	0.7027	-0.6214	-0.9181	0.0676	-0.7293	0.6923	0.648	0.143	0.4859	-0.0302	0.1824	0.4422	-0.1563	0.3957	28.428	77.9592	-106.7512
11	4.1845	-0.8049	-2.6769	2.3849	-0.6225	2.2843	-0.2773	-0.5586	0.1365	1.1004	0.1607	-0.3377	-0.0297	0.7285	0.1379	0.3774	0.0528	-0.1253	0.2113	-0.0086	0.2472	17.3221	127.8992	-73.1108
12	3.4941	-1.2161	3.1142	3.0598	-1.0708	8.358	0.0902	0.2606	-0.1077	-0.1587	0.0138	-0.2958	0.0214	0.5795	-0.124	0.076	-0.0053	0.0219	0.0952	-0.0158	0.1716	13.9686	133.1264	-93.8233
13	2.3906	-0.5579	0.6265	2.5958	0.053	2.3727	-0.0284	0.0127	-0.0317	-0.2153	0.0887	0.101	0.0214	-0.0073	-0.0804	0.0801	-0.0084	-0.0274	0.0601	-0.0009	0.0983	3.567	140.7635	-94.7331
14	7.7306	-0.4955	-2.1497	5.1388	0.1062	5.8143	0.1117	0.0167	0.0436	0.0645	-0.0294	0.4019	-0.3604	-0.4543	-0.1232	0.085	-0.0047	-0.0374	0.0287	-0.0034	0.0874	0.2342	141.9254	-92.0327
15	2.955	-0.493	1.1119	4.0312	-1.7619	4.3316	-0.3169	-0.0598	-0.0651	0.3473	0.3555	0.2848	-0.562	-0.3215	0.0285	0.0895	0.0241	-0.0222	0.1611	0.0304	0.1908	-3.0913	132.8931	-91.4561
16	2.4812	-2.8762	3.7769	3.4356	-3.9198	8.1841	0.1014	-0.134	0.1411	-0.3471	0.0847	0.6208	0.479	-0.7789	-0.1539	0.1396	-0.0427	-0.0536	0.2162	0.0319	0.472	-10.0687	129.0217	-91.3528
17	2.3249	-0.7179	0.8715	1.0535	-0.3401	3.1876	-0.0818	0.0217	-0.2298	-0.3645	0.1249	0.3546	0.2769	-0.2113	-0.0822	0.1522	-0.0694	-0.1068	0.137	0.0288	0.2353	0.0179	127.8773	-92.5255
18	5.7437	3.2588	-1.6101	6.4791	-2.1662	2.3615	-0.2397	0.0754	-0.0746	-0.4718	0.2064	0.5505	0.4282	-0.2847	-0.0066	0.1485	-0.0308	-0.0378	0.1161	-0.0078	0.2174	-0.0567	121.9348	-91.4973
19	1.4906	-0.4185	-0.6452	2.5911	-0.5091	1.2949	-0.1067	-0.2495	-0.1329	0.5073	0.0931	0.0022	-0.016	-0.0609	0.0276	0.1631	0.0363	-0.0197	0.1393	0.0275	0.1066	8.6617	128.945	-75.4236
20	5.3437	-0.0345	4.001	4.3953	-3.3489	5.7392	-0.2434	-0.846	-0.5971	0.6159	0.1721	0.4534	1.0102	-0.5479	0.085	0.752	0.0869	0.2016	0.4107	0.0988	0.2401	3.6617	124.41	-61.8899
21	7.1558	-0.0626	-5.0652	7.6894	-0.2311	5.126	-0.0368	-0.6177	0.3006	0.7946	0.1844	-0.5112	0.0338	0.5281	-0.1269	0.1803	0.0416	-0.0667	0.1339	-0.0197	0.2502	58.5657	125.9591	-69.5692
22	1.0159	-0.2216	-0.2658	0.0873	0.2273	8.4872	-0.0929	0.1484	-0.4048	-0.4934	0.0495	-0.7399	0.1697	0.4039	-0.0938	0.3001	-0.0441	0.2	0.1661	-0.0888	0.2542	60.9371	131.5539	-90.4347
23	2.4316	-0.7693	0.5178	1.5363	0.3021	0.8928	-0.0797	0.2573	-0.0092	-0.7003	0.1137	-0.0162	0.0501	0.057	-0.0224	0.2989	-0.0689	0.0413	0.1718	-0.0086	0.1307	51.3014	139.3011	-93.2758
24	6.8271	-2.8444	-3.9738	4.0861	0.3867	6.1975	0.0754	0.2831	-0.1872	-0.5965	0.0189	0.4106	-0.2781	-0.4257	-0.115	0.2844	-0.0921	0.0067	0.1713	-0.0067	0.0795	47.5262	140.8497	-92.2073
25	1.9803	-0.0434	0.8491	4.8873	-3.2555	7.8852	-0.2763	0.2155	0.1363	-0.0934	0.316	0.2161	-0.7345	-0.3863	-0.0945	0.2404	-0.0337	-0.0373	0.2078	-0.0054	0.1299	43.8633	132.0089	-92.6482
26	2.1883	-2.1983	1.9764	6.0992	-4.2292	7.1468	-0.215	0.4549	0.1075	-0.9833	0.2002	0.9516	0.301	-0.7555	-0.0886	0.3093	-0.1099	-0.117	0.2658	-0.0049	0.3114	37.3093	128.0892	-94.0548
27	2.0557	0.4488	-0.196	0.8453	0.2912	1.8558	-0.2039	0.4036	-0.2976	-0.7583	0.1803	0.0038	0.1177	-0.106	-0.0496	0.2841	-0.0853	-0.0226	0.1934	-0.0452	0.1762	46.8227	124.2375	-92.3926
28	0.6016	1.6152	-0.5602	5.777	-1.9875	0.679	-0.1542	0.0213	-0.1284	-0.2361	0.1175	0.1926	0.2187	-0.1068	0.081	0.057	0.0043	0.0241	0.1181	-0.0205	0.2055	52.3082	120.9611	-78.8592
29	3.8031	-0.5766	0.0934	3.4165	0.1611	2.4896	-0.0672	-0.0937	-0.2564	0.2032	0.101	0.0857	0.1701	-0.0524	-0.041	0.0988	0.0072	0.0256	0.0695	0.0007	0.0941	50.4112	130.4174	-72.0207
30	5.5716	3.0798	-2.1	1.7562	-0.7674	3.6395	-0.2844	-0.8	-0.9209	0.7025	0.3941	0.929	0.5842	-0.5206	0.1544	0.4066	0.0114	0.1574	0.3778	0.1698	0.4147	41.1311	124.4682	-60.5593

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 80 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 81 through 107 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 108 through 200 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 16 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 17 through 69 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 70 through 83 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 84 through 119 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 120 through 132 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 188 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 189 through 205 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 5 through 16 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 17 through 34 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 35 through 69 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 70 through 80 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 81 through 119 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 120 through 132 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 133 through 148 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 149 through 158 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 159 through 188 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 189 through 199 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 5 through 16 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 17 through 34 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 35 through 69 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 70 through 80 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 81 through 119 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 120 through 132 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 133 through 158 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 159 through 168 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 169 through 188 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 189 through 201 )

-
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