PDB-5acw: VIM-2-1, Discovery of novel inhibitor scaffolds against the metal...

ID or keywords:

Entry

Database: PDB / ID: 5acw

Title

VIM-2-1, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening

Components

BETA-LACTAMASE

Keywords

HYDROLASE

Function / homology

Function and homology information

beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.

Citation

Journal: J.Med.Chem. / Year: 2015
Title: Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 by Spr Based Fragment Screening
Authors: Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.

History

Deposition	Aug 18, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Database references
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other Category: atom_site / pdbx_database_status / struct_conn Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1	Jan 10, 2024	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 / struct_site 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5acw.cif.gz	293.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5acw.ent.gz	242.4 KB	Display	PDB format
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Validation report

Summary document	5acw_validation.pdf.gz	471.3 KB	Display	wwPDB validaton report
Full document	5acw_full_validation.pdf.gz	476 KB	Display
Data in XML	5acw_validation.xml.gz	27.7 KB	Display
Data in CIF	5acw_validation.cif.gz	42.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/5acw ftp://data.pdbj.org/pub/pdb/validation_reports/ac/5acw	HTTPS FTP

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Related structure data

Related structure data	5acuC 5acvC 5acxC 1ko3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6hf5-d 5yd7-1 4bz3-1 6kzn-2 6dd1-1 5n55-2 6tgi-2 4pvt-2 6tma-2 5mm9-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #105 - Sep 2008 Ribonuclease A similarity (2) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: BETA-LACTAMASE

B: BETA-LACTAMASE

hetero molecules

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

1

A: BETA-LACTAMASE

hetero molecules

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

2

B: BETA-LACTAMASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.540, 79.290, 67.920
Angle α, β, γ (deg.)	90.00, 130.32, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-2010- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	BETA-LACTAMASE Mass: 28400.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: 301-5473 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase

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Non-polymers , 5 types, 690 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-RHU / 4-methyl-5-(trifluoromethyl)-1,2,4-triazole-3-thiol Mass: 183.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₄F₃N₃S
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-OH / HYDROXIDE ION Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.83 Å³/Da / Density % sol: 32.97 % / Description: NONE
Crystal grow	pH: 7.2 Details: 22-27%(PEG) 3350, 0.2 M MAGNESIUM FORMATE AND 5 MM BETA-MERCAPTOETHANOL, pH 7.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.8→38.72 Å / Num. obs: 37595 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / B_iso Wilson estimate: 14.8 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 15.2
Reflection shell	Resolution: 1.8→1.85 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / % possible all: 94

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3

Resolution: 1.8→38.711 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1895	1935	5.2 %
R_work	0.1417	-	-
obs	0.1442	37595	98.8 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→38.711 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3512	0	56	674	4242

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3811
X-RAY DIFFRACTION	f_angle_d	1.172	5246
X-RAY DIFFRACTION	f_dihedral_angle_d	14.012	1385
X-RAY DIFFRACTION	f_chiral_restr	0.048	587
X-RAY DIFFRACTION	f_plane_restr	0.006	691

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 (%)
1.8-1.8451	0.3	134	0.2389	2398	X-RAY DIFFRACTION	94
1.8451-1.8949	0.2798	131	0.2174	2495	X-RAY DIFFRACTION	97
1.8949-1.9507	0.2298	119	0.1956	2513	X-RAY DIFFRACTION	97
1.9507-2.0137	0.2297	132	0.1794	2541	X-RAY DIFFRACTION	99
2.0137-2.0856	0.2245	161	0.1508	2505	X-RAY DIFFRACTION	99
2.0856-2.1691	0.1945	148	0.1468	2542	X-RAY DIFFRACTION	100
2.1691-2.2678	0.1924	177	0.1436	2555	X-RAY DIFFRACTION	100
2.2678-2.3874	0.234	111	0.1438	2580	X-RAY DIFFRACTION	100
2.3874-2.5369	0.2085	148	0.1365	2550	X-RAY DIFFRACTION	100
2.5369-2.7328	0.2138	152	0.1339	2580	X-RAY DIFFRACTION	100
2.7328-3.0077	0.1948	131	0.1318	2575	X-RAY DIFFRACTION	100
3.0077-3.4427	0.1685	111	0.1201	2608	X-RAY DIFFRACTION	100
3.4427-4.3365	0.1172	126	0.1122	2603	X-RAY DIFFRACTION	99
4.3365-38.7204	0.1589	154	0.1368	2615	X-RAY DIFFRACTION	100

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	5.0845	-1.5499	-0.2634	7.0501	0.089	0.7954	0.0902	-0.7713	-0.4963	0.6685	0.1217	0.1162	0.6105	0.4419	-0.1493	0.3588	0.0408	-0.1116	0.2586	0.0197	0.1872	-17.3567	4.038	13.579
2	6.229	1.0322	-3.2275	3.8914	-0.8339	5.0384	0.0843	-0.3198	-0.1085	0.1607	-0.0064	0.2542	0.3224	-0.0928	-0.0695	0.1583	-0.0458	-0.0371	0.1401	0.011	0.1004	-23.3075	8.3538	10.12
3	3.8622	0.0623	0.6945	3.3827	0.4374	3.8884	0.1231	-0.3121	-0.0161	0.2464	0.0114	-0.1577	0.0624	-0.0406	-0.0978	0.1082	-0.0246	-0.007	0.1298	0.0064	0.0927	-18.2254	16.2313	11.512
4	1.8986	0.1899	0.6885	1.0928	0.4074	1.6443	-0.0145	0.0035	0.0424	-0.0325	0.0099	-0.0304	-0.1121	0.073	0.0078	0.1076	-0.0135	0.0099	0.0564	0.0046	0.0762	-25.5917	17.2999	-1.0426
5	6.2858	-6.0393	4.4774	8.0621	-5.3103	3.6457	0.0115	-0.4642	-0.4153	0.4443	0.1611	0.427	0.137	-0.3905	-0.1723	0.2039	-0.0419	-0.0102	0.1346	-0.0025	0.1723	-34.4488	0.5368	2.0403
6	3.1363	-0.1456	0.3556	1.7488	-0.0722	2.6106	0.0584	0.2003	-0.2045	-0.116	-0.0083	-0.1128	0.2223	0.2318	-0.0507	0.1272	0.0153	0.0006	0.0485	-0.0242	0.1238	-25.0827	2.1831	-6.6466
7	4.7459	2.0296	0.6233	1.9391	-0.63	2.6484	0.0174	0.0736	-0.3721	0.0487	-0.0188	-0.1146	0.2509	-0.0462	0.0065	0.1616	0.0055	-0.006	0.0531	-0.0153	0.1304	-32.6166	-4.4141	-4.7143
8	2	6.5407	3.3481	3.7112	1.8997	0.9724	-5.9069	7.0845	7.8003	1.2061	-1.7837	-5.4741	-19.6478	17.1529	7.6869	1.1281	-0.3915	-0.1851	0.9061	0.1055	1.0304	-49.5159	-8.3769	-1.9375
9	2.0813	-0.2483	0.2096	2.6161	0.3893	2.0619	-0.0732	-0.0078	0.2614	-0.0416	0.081	-0.2301	-0.0732	0.5283	0.0091	0.0804	-0.001	-0.0133	0.2287	0.0126	0.1472	-35.0541	-9.5697	29.8228
10	3.6024	-0.5747	2.5326	1.0495	0.5736	2.7383	-0.0001	0.2857	0.2493	-0.0311	-0.1484	-0.0473	0.108	0.4491	0.1476	0.1081	0.04	0.0205	0.1403	0.0435	0.1248	-41.5743	-17.2392	26.3592
11	4.8509	-1.1842	1.821	2.0448	-1.9609	2.0322	-0.0059	0.4363	-0.2428	-0.3003	0.0151	0.0344	0.8369	0.6886	-0.081	0.2369	0.1113	0.0102	0.1927	-0.0244	0.1327	-44.2328	-24.0483	20.9923
12	0.8744	-0.1974	0.8331	1.5803	-0.0424	2.0647	0.0414	-0.024	-0.0702	0.0087	-0.0402	0.0572	0.1796	0.0852	0.0049	0.079	0.0066	0.008	0.0797	0.0065	0.0926	-52.2104	-15.1425	26.8977
13	1.4089	2.4995	2.5499	4.876	4.0538	4.9872	-0.1736	0.3619	0.1713	-0.3265	0.1512	-0.2778	-0.4033	0.6165	-0.0333	0.1546	-0.0252	-0.0173	0.1733	0.052	0.1879	-47.2083	-1.4357	16.3759
14	2.1138	-0.2047	0.1554	1.7744	-0.2577	4.1513	-0.0616	-0.1527	0.12	0.057	-0.0077	0.1096	-0.2544	-0.2384	0.0587	0.0954	0.0234	-0.0073	0.0486	-0.021	0.1244	-54.6323	-3.3686	26.4501
15	5.0141	-0.5651	3.2103	4.6029	-0.9466	6.6567	-0.1662	0.2262	0.2206	-0.0286	-0.0609	-0.0655	-0.3862	0.0327	0.1598	0.0918	0.0068	-0.0156	0.0451	-0.0018	0.1511	-53.7232	3.6338	17.9628
16	0	0	0	0	-0	0	0	0	0	-77384.17	-168409.7	-1280071.3649	39932.218	975495.18	168409.7927	0.141	0.0176	0.031	0.1954	0.0674	0.2572	-45.061	-10.613	16.298
17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.5963	-0.1424	0.0767	0.204	0.0898	0.2289	-42.854	-8.069	19.448
18	0	0	0	0	0	0	-77136.14	330472.88	475568.1863	-862737	-15873.67	93009.8266	-862737	-15873.67	93009.8266	0.3498	0.0144	-0.0724	0.1447	-0.0214	0.2037	-44.501	-31.354	30.472
19	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.2011	-0.0134	0.0295	0.1176	-0.0262	0.1571	-34.503	10.098	3.178
20	0	0	-0	0	-0	0	-2404.645	-28531.27	-296141.0083	-9618.582	-114125	-1184564.033	176241.04	738427.31	116529.733	0.2664	-0.0185	0.0306	0.2252	0.1691	0.5353	-31.203	7.859	5.283
21	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.2353	-0.0187	-0.044	0.0916	-0.0068	0.257	-20.695	30.641	0.976
22	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.3667	-0.0461	-0.0132	0.0463	0.0287	0.2398	-21.402	30.027	3.031
23	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.5166	-0.0324	0.1034	0.0786	-0.0227	0.4369	-42.446	-30.944	29.988
24	5.5286	0.9377	-2.9869	4.9299	1.9102	2.8384	1.0393	1.2447	-0.131	-0.8282	-0.678	-0.4671	-3.1669	-2.8198	-0.3515	0.4776	0.0554	-0.0586	0.3391	-0.0038	0.2342	-34.6595	9.4114	7.0456
25	5.5003	-0.9631	-4.9104	4.8166	3.181	5.5431	0.7023	3.8985	-0.906	-0.2654	-1.0685	0.6022	-0.8505	-2.6523	0.279	0.216	0.0148	0.0421	0.422	-0.0549	0.205	-41.3346	-9.58	15.7924
26	4.6482	3.5243	2.9845	5.9413	1.1822	4.276	-1.9605	-3.2457	0.8118	0.2616	1.5974	1.0519	-3.0962	-1.8242	0.3576	0.3297	0.1407	-0.0487	0.3616	-0.0598	0.3858	-16.8786	29.6074	0.8225
27	1.9158	-2.0736	0.504	6.688	-1.9447	0.5733	0.201	0.4412	-1.9982	-0.6182	1.5395	-0.3828	-0.5909	3.8658	-1.74	0.5548	-0.0386	-0.0844	0.5977	-0.1323	0.3265	-44.5041	-30.4138	34.3401
28	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.2625	0.0236	-0.0131	0.0148	-0.0223	0.151	-44.842	-30.738	32.406
29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0.0583	0.0087	-0.0444	0.0279	-0.0147	0.3656	-18.483	30.224	0.738

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 29 THROUGH 51 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 52 THROUGH 76 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 77 THROUGH 103 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 104 THROUGH 222 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 223 THROUGH 238 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 239 THROUGH 279 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 280 THROUGH 296 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 297 THROUGH 297 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 29 THROUGH 103 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 104 THROUGH 124 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 125 THROUGH 149 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 150 THROUGH 222 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 223 THROUGH 238 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 239 THROUGH 279 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 280 THROUGH 297 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 1 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 2 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 3 )
19	X-RAY DIFFRACTION	19	CHAIN 'A' AND (RESID 1 )
20	X-RAY DIFFRACTION	20	CHAIN 'A' AND (RESID 2 )
21	X-RAY DIFFRACTION	21	CHAIN 'A' AND (RESID 3 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 1 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 2 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 1 )
25	X-RAY DIFFRACTION	25	CHAIN 'C' AND (RESID 2 )
26	X-RAY DIFFRACTION	26	CHAIN 'C' AND (RESID 3 )
27	X-RAY DIFFRACTION	27	CHAIN 'C' AND (RESID 4 )
28	X-RAY DIFFRACTION	28	CHAIN 'D' AND (RESID 3 )
29	X-RAY DIFFRACTION	29	CHAIN 'D' AND (RESID 4 )

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