PDB-7ulv: Human DDAH1 soaked with its inactivator S-((4-chloropyridin-2-yl)...

ID or keywords:

Entry

Database: PDB / ID: 7ulv

Title

Human DDAH1 soaked with its inactivator S-((4-chloropyridin-2-yl)methyl)-L-cysteine

Components

N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

Keywords

HYDROLASE / DDAH1 / Dimethylargininase / DDAH / inactivator / S-((4-chloropyridin-2-yl)methyl)-L-cysteine

Function / homology

Function and homology information

dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / nitric oxide metabolic process / amino acid binding / catalytic activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Zheng, Y. / Butrin, A. / Tuley, A. / Liu, D. / Fast, W.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Optimization of a switchable electrophile fragment into a potent and selective covalent inhibitor of human DDAH1
Authors: Tuley, A. / Zheng, Y. / Tommasi, S. / Butrin, A. / May, K.V. / Ahn, Y. / Reidl, T.C. / Weerakoon, L. / Hulin, J. / Meech, R. / Patel, D.S. / Horton, C.P. / Swartzel, C.J. / Kim, Y. / ...

History

Deposition	Apr 5, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7ulv.cif.gz	635.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7ulv.ent.gz	526.2 KB	Display	PDB format
PDBx/mmJSON format	7ulv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7ulv_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	7ulv_full_validation.pdf.gz	1.9 MB	Display
Data in XML	7ulv_validation.xml.gz	67.7 KB	Display
Data in CIF	7ulv_validation.cif.gz	91.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ul/7ulv ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ulv	HTTPS FTP

-
Related structure data

Related structure data	7uluC 7ulxC 3p8eS S: Starting model for refinement C: citing same article (ref.)
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	#44 - Aug 2003 Calmodulin similarity (1) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #206 - Feb 2017 Globin Evolution similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

C: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

D: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

E: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

F: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

203 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

defined by author
Evidence: gel filtration
33.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

3

C: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

4

D: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

5

E: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

6

F: N(G),N(G)-dimethylarginine dimethylaminohydrolase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	46.404, 220.991, 73.645
Angle α, β, γ (deg.)	90.000, 91.080, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 / Dimethylarginine dimethylaminohydrolase 1 / DDAHI / Dimethylargininase-1 Mass: 33623.492 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDAH1, DDAH / Production host: Escherichia coli (E. coli) / References: UniProt: O94760, dimethylargininase
#2: Chemical	ChemComp-NO6 / S-[(pyridin-2-yl)methyl]-L-cysteine Mass: 212.269 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₉H₁₂N₂O₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 509 / 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: 1.87 Å³/Da / Density % sol: 34.27 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method ...Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method (Hampton Research, Aliso Viejo, CA) from 25 % (w/v) PEG6000, 0.1 M Tris-HCl, pH 8.2. Further optimization was done manually using a 1:1 well solution: DDAH1 stock solution ratio to improve crystal size and morphology. Crystals grew to their maximum size in 3 weeks and were harvested after approximately 25 days. To determine the structure of DDAH1 in complex with ligand, the crystals were transferred to a reservoir containing 20 uL of 20 mM of the ligand in the crystallization mother liquor (25% PEG 6000, 0.1 M Tris-HCl, pH 8.2) and soaked for 30 min. Before data collection, crystals with good size and morphology were transferred into a cryoprotection solution (Well Solution supplemented with 25 % (v/v) glycerol) for 1 to 5 seconds using a the cryoloop (Hampton Research, Laguna Niguel, CA). Individual hDDAH1:ligand crystals were flash frozen in liquid nitrogen before use.

Crystal

Density Matthews: 1.87 Å³/Da / Density % sol: 34.27 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop
Details: Purified DDAH1 was concentrated to approximately 10 mg/mL using an Amicon-Ultra centrifugal filter device (10 kDa MWCO). The protein was crystallized at 25 C using the hanging drop method ...

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.97872 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 19, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection twin

Operator: h,-k,-l / Fraction: 0.18

Reflection

Resolution: 2.37→73.66 Å / Num. obs: 59571 / % possible obs: 99.1 % / Redundancy: 4.3 % / R_pim(I) all: 0.062 / R_rim(I) all: 0.128 / Net I/σ(I): 8 / Num. measured all: 256173

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Mean I/σ(I) obs	Num. measured all	Num. unique obs	R_pim(I) all	R_rim(I) all	% possible all
2.37-2.41	4.3	3.5	12131	2820	0.406	0.836	94.1
6.42-73.7	4.2	13	12756	3057	0.036	0.073	100

-
Processing

Software

Name	Version	Classification
xia2		data scaling
PHENIX	1.19.2_4158	refinement
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3P8E

3p8e

Resolution: 2.37→73.63 Å / Cross valid method: THROUGHOUT / σ(F): 1.68 / Phase error: 36.67 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2692	2926	4.99 %
R_work	0.237	56622	-
obs	0.2418	59548	99.02 %

Solvent computation

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

Displacement parameters

B_iso max: 99.33 Å² / B_iso mean: 45.4034 Å² / B_iso min: 15.98 Å²

Refinement step

Cycle: final / Resolution: 2.37→73.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12606	0	0	509	13115
B_iso mean	-	-	-	41.95	-
Num. residues	-	-	-	-	1632

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.37-2.41	0.3746	130	0.3571	2689	2819	90
2.41-2.45	0.4021	132	0.3478	2875	3007	94
2.45-2.5	0.3824	150	0.3398	2773	2923	94
2.5-2.55	0.3743	157	0.3369	2821	2978	94
2.55-2.6	0.339	152	0.3307	2840	2992	94
2.6-2.67	0.3555	182	0.3275	2763	2945	93
2.67-2.73	0.3308	155	0.3264	2836	2991	93
2.73-2.81	0.3391	136	0.32	2797	2933	95
2.81-2.89	0.2962	154	0.3127	2847	3001	94
2.89-2.98	0.3417	117	0.3038	2844	2961	96
2.98-3.09	0.2918	169	0.2791	2860	3029	93
3.09-3.21	0.3042	133	0.2653	2801	2934	95
3.21-3.36	0.3247	156	0.2542	2848	3004	94
3.36-3.54	0.2403	134	0.2321	2853	2987	95
3.54-3.76	0.2439	133	0.2232	2853	2986	95
3.76-4.05	0.2354	138	0.2068	2845	2983	95
4.05-4.45	0.2362	157	0.1885	2843	3000	94
4.45-5.1	0.2137	139	0.1798	2897	3036	95
5.1-6.42	0.2263	152	0.2094	2845	2997	95
6.42-73.63	0.2326	150	0.1729	2892	3042	95

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	0.1469	0.0384	0.228	0.5887	0.2287	1.1611	0.0137	-0.0336	0.0287	0.0387	0.0344	0.0354	-0.054	-0.0461	0.0071	0.3822	0.0455	-0.0509	0.7123	0.0776	0.1207	-4.7419	-18.7481	1.1232
2	0.1026	0.0328	-0.1043	0.3331	-0.1046	0.7831	0.0134	-0.0121	0.0351	0.2606	-0.0097	-0.0051	-0.1615	-0.0297	0.0491	0.469	0.0493	-0.0778	0.8533	0.0181	-0.0163	7.4928	-17.1034	12.5068
3	0.3507	0.0144	0.5582	0.8271	0.2587	1.6307	-0.0052	-0.1251	-0.0123	0.2153	-0.0152	-0.0143	0.1205	-0.0285	0.0182	0.4411	0.0302	-0.0631	0.73	0.0173	0.1236	1.2117	-34.7343	14.5211
4	0.3403	0.4403	0.047	1.2774	0.3233	1.3324	-0.0129	-0.013	-0.0035	0.057	0.0175	0.0143	0.1014	-0.0236	0.0081	0.389	0.053	0.022	0.6879	0.0296	0.0347	-8.2919	-28.9362	8.1396
5	0.4366	0.1114	0.0559	0.7183	0.5056	1.4908	-0.0346	0.0018	-0.0365	-0.0355	-0.0047	-0.0051	0.1298	0.0698	-0.0219	0.3129	0.0798	-0.0143	0.7572	0.0423	0.0217	17.6969	-25.579	-16.0875
6	0.4366	0.6217	0.8036	1.1592	1.4303	1.954	-0.0472	0.1211	-0.0498	-0.2071	-0.0083	-0.011	0.2955	0.0226	0.0527	0.4664	0.0819	0.0366	0.7478	0.0083	0.1094	27.8653	-33.7594	-25.3213
7	0.2131	-0.0707	-0.222	0.3826	-0.0425	0.8819	-0.0099	0.0187	-0.0279	-0.0395	0.0265	-0.0873	0.1178	0.3504	-0.0015	0.3345	0.0963	0.0612	0.9487	-0.0321	0.1498	35.8054	-23.7804	-31.0102
8	1.4977	-1.2251	-0.1188	1.7394	-1.3015	2.6619	-0.0297	-0.028	0.0458	0.0807	0.0251	-0.1638	-0.0905	0.4617	0.0144	0.2416	0.019	0.0265	0.835	0.0324	0.1885	29.2134	-13.7873	-24.9681
9	0.3589	0.1003	-0.1912	0.1523	0.104	0.4138	-0.0355	0.0893	-0.0179	-0.1268	0.0294	-0.1108	-0.0498	0.4017	-0.0018	0.3898	-0.0583	0.0043	0.8979	0.0773	0.1874	30.7532	-7.3797	-32.3878
10	0.0395	0.0334	-0.2307	0.7616	0.363	1.8228	-0.0075	0.166	0.0173	-0.1859	-0.0052	0.0329	0.01	0.1352	0.0065	0.3575	0.0115	-0.0875	0.8237	0.0399	0.1945	20.1035	-12.3114	-32.8103
11	0.2717	-0.0816	0.2242	1.8723	0.3531	1.6259	-0.0433	0.0646	0.0147	-0.3075	0.0774	0.0763	-0.0937	-0.0023	-0.0276	0.2971	0.0392	-0.0427	0.7105	0.0639	0.0599	15.8136	-14.0313	-23.7402
12	0.8969	0.0909	0.8908	0.8588	0.059	0.8916	-0.0605	-0.2223	0.0979	0.0571	0.0095	0.1049	-0.07	-0.3576	0.066	0.4748	0.0565	-0.1244	0.8267	0.0067	0.1535	2.9368	22.5006	-6.7268
13	0.3326	0.0775	0.2277	0.4151	0.1544	0.1826	-0.0811	0.1208	0.1477	-0.2793	-0.0076	0.1287	-0.1391	-0.1342	0.1528	0.5981	0.0283	-0.2365	0.8916	0.0619	0.2466	-9.3028	17.9229	-16.5751
14	0.1727	0.2294	0.3719	1.2169	0.471	1.1878	-0.019	0.1079	-0.0663	-0.13	0.0203	0.0298	0.1025	-0.2432	0.0117	0.4788	-0.0139	-0.0087	0.791	0.0321	0.1689	2.353	3.3022	-14.293
15	0.8878	-0.641	0.5253	1.1659	-0.1197	2.3752	-0.0985	-0.1898	-0.05	-0.0604	0.0972	0.0619	0.1275	-0.0976	-0.0246	0.3984	0.0362	-0.0086	0.7019	0.1088	0.1484	10.6544	10.977	-8.4181
16	0.5314	-0.0329	0.0221	0.9746	0.1316	1.312	-0.0225	0.0352	0.0148	0.2391	-0.0735	0.043	-0.0006	0.1132	0.0055	0.3672	0.0501	0.0953	0.7307	-0.0204	0.1068	4.3012	-53.8641	-1.7581
17	1.5691	-0.3951	-0.0704	2.0967	0.0556	5.3245	0.0171	0.3051	0.1147	-0.3575	-0.0411	-0.1294	-0.2413	0.4584	0.0546	0.4273	0.0371	-0.0703	0.6818	0.0047	0.1306	-8.703	-51.4217	-10.4108
18	0.0502	0.087	0.1382	0.1734	0.1769	0.8664	0.0956	0.1127	-0.0238	-0.0624	0.0108	0.0315	0.0526	-0.1181	0.0089	0.4198	0.0306	-0.1304	1.0895	-0.0526	0.1696	-7.1687	-60.2876	-16.3443
19	0.4279	-0.3603	0.1308	0.8307	-0.1449	1.8786	0.0166	0.2461	-0.0427	-0.3301	-0.0365	-0.0947	0.1023	0.1516	0.0403	0.3896	0.0235	0.0213	0.887	-0.0643	0.1067	9.1564	-64.5419	-12.5019
20	0.6577	-0.1672	0.0644	1.1015	-0.5736	2.0169	-0.0079	0.053	0.002	0.1701	-0.0086	0.0024	0.1178	-0.0678	0.0025	0.4395	-0.0348	-0.0084	0.773	0.0107	0.1104	28.3986	-64.9019	14.8576
21	0.3122	-0.4292	0.0952	0.7704	-0.3263	0.8674	0.0843	-0.0231	-0.0491	0.0272	-0.0088	0.0161	0.2945	0.0099	-0.0401	0.5045	-0.1102	-0.0252	0.7234	0.0156	0.1193	16.9242	-70.6635	22.6886
22	1.2348	-0.0998	-1.4656	1.1734	-0.5919	2.8662	-0.0199	0.0213	-0.044	0.2606	0.1619	0.2377	0.1786	-0.6349	-0.1243	0.5273	-0.1053	0.0611	0.8058	0.0648	0.2067	12.4136	-63.426	31.0047
23	0.744	-0.2427	-0.1658	1.2962	0.1235	1.7718	0.108	-0.1844	-0.0436	0.3459	0.0129	-0.0125	-0.0745	0.0538	-0.0853	0.6373	-0.0372	-0.0369	0.8759	-0.0254	0.1236	28.0677	-52.5798	27.7794
24	0.2764	0.0791	-0.0504	0.5016	0.0186	1.5067	-0.0398	0.1121	0.0298	-0.2544	0.0748	0.03	-0.2805	-0.0919	-0.0713	0.5815	0.0057	0.0597	1.0702	0.0489	0.2209	30.7188	12.7474	13.6862
25	0.9011	-0.307	0.5166	1.9203	-0.1025	3.3207	0.124	0.1241	-0.0507	-0.1799	-0.112	-0.0915	0.4523	0.3962	-0.0169	0.5021	0.0092	-0.069	0.7911	-0.0107	0.1094	21.7987	2.1718	19.5567
26	0.1118	0.0206	-0.1062	0.7723	-0.4859	1.6614	0.0001	0.0702	0.0146	0.0217	-0.0556	0.0289	-0.1836	-0.0876	0.0009	0.4496	0.0478	-0.0236	0.7975	0.0593	0.0752	18.1818	15.2653	31.2169
27	0.6443	0.026	-1.1341	1.0909	0.1933	2.2639	0.1668	-0.0215	0.086	0.0107	-0.2336	-0.1654	-0.2102	0.4322	0.0493	0.4579	-0.0473	0.0491	1.0866	0.1573	0.2477	31.6659	21.7271	24.0743

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 54 )	A	9 - 54
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 167 )	A	55 - 167
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 168 through 230 )	A	168 - 230
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 231 through 282 )	A	231 - 282
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 77 )	B	9 - 77
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 78 through 118 )	B	78 - 118
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 119 through 167 )	B	119 - 167
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 168 through 182 )	B	168 - 182
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 183 through 204 )	B	183 - 204
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 205 through 230 )	B	205 - 230
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 231 through 282 )	B	231 - 282
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 9 through 95 )	C	9 - 95
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 96 through 167 )	C	96 - 167
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 168 through 230 )	C	168 - 230
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 231 through 282 )	C	231 - 282
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 9 through 80 )	D	9 - 80
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 81 through 101 )	D	81 - 101
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 102 through 204 )	D	102 - 204
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 205 through 282 )	D	205 - 282
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 9 through 76 )	E	9 - 76
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 77 through 111 )	E	77 - 111
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 112 through 167 )	E	112 - 167
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 168 through 282 )	E	168 - 282
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 9 through 71 )	F	9 - 71
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 72 through 118 )	F	72 - 118
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 119 through 230 )	F	119 - 230
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 231 through 282 )	F	231 - 282

-
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