PDB-4rad: Aza-acyclic nucleoside phosphonates containing a second phosphona...

ID or keywords:

Entry

Database: PDB / ID: 4rad

Title

Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents

Components

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / Hypoxanthine-guanine phosphoribosyltransferase / Acyclic nucleoside monophosphonates / Malaria / 6-Oxopurine Phosphoribosyltransferase / 9-[(N-Phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]guanine / cytoplasmic / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine salvage / hypoxanthine metabolic process / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / hypoxanthine phosphoribosyltransferase / lymphocyte proliferation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Keough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.-H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.

Citation

Journal: J.Med.Chem. / Year: 2015
Title: Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs ...
Authors: Keough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.

History

Deposition	Sep 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 7, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 11, 2015	Group: Database references
Revision 1.2	Dec 23, 2015	Group: Structure summary
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rad.cif.gz	948.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4rad.ent.gz	816.3 KB	Display	PDB format
PDBx/mmJSON format	4rad.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rad_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	4rad_full_validation.pdf.gz	4.5 MB	Display
Data in XML	4rad_validation.xml.gz	66.7 KB	Display
Data in CIF	4rad_validation.cif.gz	88.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/4rad ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4rad	HTTPS FTP

-
Related structure data

Related structure data	4rabC 4racC 4ranC 4raoC 4raqC C: citing same article (ref.)
Similar structure data	5w8v-d 4rac-d 4ran-d 4rao-d 4rab-d 5fp1-d 4raq-d 6bnj-d 4ijq-d 6fok-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	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (9)

Deposited unit

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

E: Hypoxanthine-guanine phosphoribosyltransferase

F: Hypoxanthine-guanine phosphoribosyltransferase

G: Hypoxanthine-guanine phosphoribosyltransferase

H: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

1

A: Hypoxanthine-guanine phosphoribosyltransferase

B: Hypoxanthine-guanine phosphoribosyltransferase

C: Hypoxanthine-guanine phosphoribosyltransferase

D: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

2

E: Hypoxanthine-guanine phosphoribosyltransferase

F: Hypoxanthine-guanine phosphoribosyltransferase

G: Hypoxanthine-guanine phosphoribosyltransferase

H: Hypoxanthine-guanine phosphoribosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.048, 114.930, 97.536
Angle α, β, γ (deg.)	90.00, 101.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hypoxanthine-guanine phosphoribosyltransferase / HGPRT / HGPRTase Mass: 24481.217 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical	ChemComp-3L5 / (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid Mass: 454.313 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₃H₂₄N₆O₈P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.13 Å³/Da / Density % sol: 42.37 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 8 Details: 1 M sodium/potassium tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP

-
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: Jan 1, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95369 Å / Relative weight: 1
Reflection	Resolution: 2→35.56 Å / Num. obs: 109369 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→35.56 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 28.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2592	1998	1.83 %
R_work	0.2092	-	-
obs	0.2101	109325	98.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→35.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12792	0	241	598	13631

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	13425
X-RAY DIFFRACTION	f_angle_d	0.919	18176
X-RAY DIFFRACTION	f_dihedral_angle_d	15.748	5126
X-RAY DIFFRACTION	f_chiral_restr	0.032	2012
X-RAY DIFFRACTION	f_plane_restr	0.003	2260

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 (%)
2-2.05	0.3365	144	0.3077	7692	X-RAY DIFFRACTION	100
2.05-2.1054	0.3144	143	0.2792	7711	X-RAY DIFFRACTION	99
2.1054-2.1674	0.2885	143	0.2678	7682	X-RAY DIFFRACTION	99
2.1674-2.2373	0.2942	143	0.2664	7679	X-RAY DIFFRACTION	99
2.2373-2.3173	0.3557	143	0.2648	7694	X-RAY DIFFRACTION	99
2.3173-2.41	0.2866	143	0.2529	7679	X-RAY DIFFRACTION	99
2.41-2.5197	0.2938	144	0.2554	7688	X-RAY DIFFRACTION	99
2.5197-2.6525	0.3425	142	0.2519	7656	X-RAY DIFFRACTION	99
2.6525-2.8186	0.2695	143	0.2465	7650	X-RAY DIFFRACTION	98
2.8186-3.0361	0.3239	142	0.2295	7619	X-RAY DIFFRACTION	98
3.0361-3.3415	0.2602	143	0.2129	7631	X-RAY DIFFRACTION	98
3.3415-3.8245	0.2652	141	0.1837	7625	X-RAY DIFFRACTION	98
3.8245-4.8166	0.2036	143	0.1547	7654	X-RAY DIFFRACTION	98
4.8166-35.56	0.195	141	0.1785	7667	X-RAY DIFFRACTION	97

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	1.8961	-0.012	-0.5626	2.4132	-0.1572	2.0151	-0.0522	-0.03	-0.0575	0.0274	0.0009	0.1953	0.0437	-0.0614	0.0405	0.2214	-0.0049	-0.0053	0.2684	-0.0228	0.3266	81.2572	-25.1287	2.3628
2	2.0048	1.7041	-1.7448	3.4278	-3.6662	6.6616	0.1512	-0.2263	0.8115	0.0491	0.0983	0.0556	-0.4987	0.1013	-0.405	0.3812	0.0129	-0.0313	0.3195	-0.0573	0.5437	79.6617	-4.9309	-0.3268
3	4.666	-1.299	0.2172	6.7653	-1.5533	2.6058	-0.0372	0.1774	0.1663	-0.1807	-0.0615	0.2501	-0.2381	-0.2658	0.0888	0.2838	0.0375	-0.0561	0.2758	-0.0113	0.3313	70.3272	-12.6637	-2.8049
4	1.3142	-0.5372	0.6403	2.0397	-0.439	6.4752	-0.1658	-0.1648	-0.1036	-0.0166	-0.0715	0.5211	0.084	-0.6677	0.1422	0.226	0.0016	-0.0065	0.3413	-0.0637	0.4592	69.6546	-25.6489	4.5348
5	0.6832	-0.8049	-1.9566	1.471	1.7953	6.5022	-0.6727	-0.0305	-0.3642	0.6346	0.0026	0.4871	0.6194	-0.8891	0.5565	0.4407	0.009	0.1295	0.4352	-0.0215	0.5017	72.2681	-29.7587	17.3052
6	4.5339	1.0676	-1.3873	6.7783	-4.1654	5.3041	-0.0485	0.4323	-0.2848	-0.405	0.1422	0.5901	0.242	-0.2917	-0.0549	0.2811	-0.0342	-0.0318	0.344	-0.0936	0.3544	84.8863	-39.3067	-7.8909
7	1.8214	-0.5269	0.1139	2.3018	1.0421	3.0401	-0.1201	-0.2371	-0.0382	0.2853	0.1679	-0.0686	0.205	0.1219	-0.0407	0.2849	0.0271	0.0079	0.2915	0.0204	0.2773	98.7702	-38.6692	10.5801
8	4.3697	-0.4288	0.585	5.9218	2.5663	2.3744	-0.3722	-0.382	-0.3349	0.771	-0.1984	0.1518	0.7064	-0.2907	0.4659	0.36	0.0418	0.0156	0.4136	0.0248	0.4069	106.9285	-40.3741	12.1765
9	8.7381	-3.7226	1.8678	7.7162	-4.8123	7.1416	-1.2104	-0.4104	-0.4025	0.3482	-0.81	0.688	0.7206	-0.7974	2.1006	0.5581	0.0297	0.1684	0.6422	-0.0949	0.8392	114.1624	-52.994	-0.3345
10	6.3464	0.7803	4.3014	3.3952	1.6871	6.5188	0.04	0.1263	-0.7546	0.3887	0.2104	-0.4387	0.529	0.7019	-0.3211	0.3432	0.0926	0.0325	0.3844	0.051	0.4309	104.3858	-52.4484	8.575
11	5.4996	6.9222	5.5879	9.624	7.188	5.7446	0.1862	-0.0576	-0.8243	0.4789	-0.1006	-0.2228	0.8569	0.0023	-0.2608	0.4334	0.0305	0.0832	0.3222	0.0311	0.4387	92.9884	-55.5571	5.9466
12	4.539	-1.0831	-1.5878	2.7416	-0.6607	7.2414	-0.0896	0.4595	-0.2214	-0.5074	0.0512	0.0129	0.5082	-0.2114	0.0592	0.3274	-0.0421	-0.0062	0.2934	-0.0617	0.3024	93.5504	-43.9358	-10.9937
13	6.325	-0.8689	-0.2531	1.9835	2.2822	5.766	-0.0495	0.1218	0.9784	-0.2207	0.1974	-0.3539	-0.6227	0.3845	-0.0788	0.3267	-0.0823	0.0049	0.3179	0.0101	0.5625	104.2796	-5.9191	3.7566
14	3.0083	0.7386	-0.7955	4.0777	-0.5834	1.4285	-0.0526	-0.2175	-0.0108	0.1497	0.0334	0.1163	0.0493	0.0504	0.0215	0.246	-0.0011	-0.0387	0.2804	-0.0432	0.2373	90.5329	-17.6305	17.8391
15	4.7796	-3.0551	-1.4743	4.5015	2.0876	2.3853	-0.3985	-0.4286	-0.1601	0.5037	0.2643	0.4791	0.0396	0.0927	0.1848	0.3516	-0.0349	-0.001	0.4302	-0.0479	0.2968	82.6793	-19.618	19.8256
16	3.4192	-1.1245	1.7446	6.3325	-4.2863	4.1834	-0.5161	-0.4802	0.6546	0.5286	-0.4182	0.134	-0.7462	-0.8615	0.8869	0.4153	-0.0373	-0.0581	0.5954	-0.056	0.7838	74.5539	-7.6704	23.2275
17	7.3918	2.6304	-5.0213	2.9973	-2.3531	4.8654	0.327	-0.6083	0.7308	-0.024	-0.1159	0.415	-0.4505	0.1129	-0.2173	0.3049	-0.0334	-0.0488	0.3754	-0.0651	0.4209	85.253	-3.5524	24.2531
18	1.7825	-0.9303	-0.949	0.7644	0.5077	2.1577	-0.2552	-0.206	0.2613	0.2771	0.2483	-0.212	-0.0326	-0.0053	-0.0391	0.3865	0.0091	-0.0483	0.4187	-0.0796	0.369	93.1943	-4.9408	24.4325
19	1.8637	-0.423	-0.005	1.6026	-1.1382	3.1285	0.027	-0.1163	0.8095	-0.1011	-0.0522	0.143	-0.12	0.0625	-0.001	0.3017	0.0007	-0.0026	0.2761	-0.0349	0.5419	95.5365	-1.5219	8.2892
20	5.9477	0.1956	1.6822	2.6362	0.2834	8.4155	-0.1988	0.9676	1.2287	-0.012	-0.0858	0.1803	-0.9565	0.0929	0.1475	0.3419	-0.0558	-0.0423	0.4172	0.1286	0.6134	96.2657	-0.713	0.6869
21	2.9209	-0.3873	-2.2045	3.1699	-0.0882	4.1116	0.063	-0.489	0.524	0.5501	0.2072	-0.27	-0.273	0.5231	-0.182	0.3346	0.0081	-0.1289	0.4474	-0.1112	0.4434	112.3573	-19.6387	15.4697
22	1.6333	0.0116	0.5954	2.6865	1.2989	2.7857	-0.1406	0.1637	0.1961	-0.2765	0.0767	-0.0253	-0.182	0.0309	0.0585	0.2489	-0.0682	0.0123	0.2987	0.0082	0.2694	105.1901	-26.1673	-5.6604
23	3.4442	-1.9461	1.1372	4.4562	-1.3463	4.7712	0.0378	0.1649	0.708	-0.463	-0.1336	-0.374	-0.1843	-0.3376	-0.0641	0.365	-0.0487	0.0462	0.4373	-0.0328	0.3464	104.512	-33.7709	-11.2626
24	1.4036	-0.041	-0.9092	3.5144	1.1494	2.7255	-0.1631	0.214	-0.1836	-0.2997	0.3328	-0.5154	0.2711	0.4619	-0.1898	0.3109	-0.0365	0.0702	0.4663	-0.1152	0.3992	118.4661	-32.5547	-9.9628
25	1.4126	0.5867	0.6199	3.4458	-0.719	3.1301	-0.1209	-0.0416	-0.0022	0.1703	0.0732	-0.7094	-0.109	0.5825	0.0772	0.2359	0.0112	-0.0037	0.4664	-0.0989	0.4977	120.2515	-24.4594	4.271
26	2.5476	0.5103	0.9401	3.9196	-2.1156	4.5014	-0.1083	-0.331	0.3263	0.6695	-0.0373	-1.0448	0.4148	0.9993	0.1638	0.4277	0.1213	-0.1364	0.6034	-0.0971	0.4885	116.7211	-29.8038	17.5129
27	8.5881	1.3939	-8.357	6.4618	1.9188	9.6223	0.7201	-0.2145	1.0279	0.5319	-0.4224	0.5358	-0.2905	0.4345	-0.2875	0.4017	-0.0353	-0.0975	0.3344	-0.0044	0.4501	63.856	-48.6326	46.0128
28	2.2048	0.7247	0.3466	3.2721	-1.1027	4.7425	0.0949	-0.0289	-0.2549	-0.0929	-0.0246	0.1915	-0.0552	-0.0485	-0.0961	0.2773	0.0192	-0.0736	0.2554	-0.0166	0.3633	71.9739	-59.9956	45.0824
29	8.3627	3.6333	2.9975	3.8344	0.6221	3.0213	0.0565	-0.2329	-0.4197	-0.168	-0.017	0.1366	0.0787	-0.323	-0.0787	0.3642	0.0007	-0.0619	0.3302	0.0375	0.509	72.0791	-72.2421	49.9214
30	3.1316	0.3289	0.9066	7.2774	-3.6505	4.456	0.246	-0.2175	-0.5864	-0.3581	0.0041	0.3521	0.6338	-0.264	-0.2745	0.4756	-0.0812	-0.1337	0.3701	0.0586	0.5579	61.9567	-74.1033	52.083
31	3.2348	-0.0896	-1.5842	3.2235	-0.5258	6.1538	-0.0009	0.4509	-0.2764	-0.5448	-0.0714	0.254	0.246	-0.6378	0.0343	0.402	-0.0222	-0.1571	0.3767	-0.0445	0.4122	63.2742	-59.5162	37.5021
32	3.1158	-2.836	3.1065	5.8862	-5.162	4.5544	-0.1408	0.2134	0.3163	0.2745	0.6543	0.9185	-0.2206	-1.0038	-0.5512	0.3873	0.0663	0.0175	0.3743	-0.0319	0.4604	71.3957	-39.838	46.2636
33	3.1948	0.5645	-0.6764	1.928	-0.3138	3.1404	-0.0132	0.1688	0.0431	-0.1782	-0.0305	-0.0195	0.1492	-0.2032	0.0481	0.2517	0.0602	-0.0071	0.1966	0.0156	0.2424	84.2106	-45.8026	46.5008
34	3.9313	3.2243	4.8288	5.5058	5.1079	9.7446	-0.0022	0.0282	-0.221	-0.2954	0.1727	-0.2595	0.1315	0.2277	-0.2854	0.344	0.0515	0.0235	0.2434	0.0275	0.272	92.0197	-49.6021	41.4929
35	6.0893	1.7002	-0.1759	3.0035	-0.6772	0.2687	-0.1059	0.5622	0.1371	-0.4471	-0.0823	0.1546	-0.1542	0.0937	0.0098	0.4564	0.0816	0.0346	0.3676	0.093	0.3252	98.2509	-46.1164	39.4152
36	0.7926	-0.2197	1.2108	3.3286	2.0282	3.5399	0.308	-0.3258	0.3677	-0.2756	0.2172	-0.9301	-0.7369	1.1542	-0.4302	0.34	-0.0189	-0.0332	0.7293	0.0512	0.8022	103.4541	-33.1473	44.8338
37	5.4831	-0.747	-1.5489	5.021	1.5198	0.9432	-0.1313	0.0464	0.356	-0.3346	-0.044	-0.0011	-0.2891	0.1286	0.1611	0.3848	0.0255	-0.0236	0.316	0.082	0.2857	91.0928	-34.673	43.0115
38	7.891	-4.522	-4.9398	9.8521	4.6074	3.5205	0.373	0.2375	1.0839	-0.6894	0.2629	-0.4225	-0.7082	0.1016	-0.7099	0.4926	-0.0909	0.0212	0.3997	0.002	0.4741	98.186	-28.3161	41.5359
39	8.9474	0.3478	-5.4047	5.5221	-0.9461	6.1464	-0.0353	0.2402	0.0559	-0.5072	-0.2473	-0.4352	-0.0455	0.4133	0.276	0.345	-0.001	-0.0495	0.3406	0.0855	0.3176	92.3022	-35.0723	37.8262
40	6.1151	-7.5667	-5.3251	9.4628	6.8922	4.9546	0.1597	0.1448	0.9764	-0.4981	0.2104	-0.7367	-0.2431	-0.0971	-0.4086	0.4402	-0.003	-0.0435	0.3346	0.0675	0.4156	82.8944	-31.6585	40.4107
41	3.6308	0.8984	2.4614	1.663	-0.3977	4.2888	0.06	-0.3733	0.0969	0.0777	-0.1133	-0.0519	-0.0774	-0.2012	-0	0.2471	0.0252	0.0016	0.2866	-0.0114	0.2388	82.0492	-39.0487	58.2947
42	2.7007	-3.0712	-3.6546	5.5462	4.6615	4.9497	0.2074	0.0867	-0.5384	0.5983	0.4671	-0.5794	1.77	0.7563	-0.4986	0.6338	0.0795	0.0829	0.3656	-0.1046	1.1543	100.6543	-79.3334	45.1643
43	3.6252	0.2548	0.3418	2.5661	1.1795	2.6205	-0.0135	-0.0731	-0.7308	-0.1844	-0.2254	-0.5649	0.0281	0.3037	0.1776	0.4214	0.0557	0.0063	0.2595	-0.0013	0.6068	91.1579	-72.5031	45.7114
44	4.4973	2.2791	-1.0474	7.125	-1.0606	0.3751	-0.0306	0.2706	-0.3776	-0.6818	0.0565	-0.1123	0.3673	-0.1045	-0.0417	0.541	0.0173	-0.0613	0.3364	-0.092	0.4106	79.753	-70.1135	34.4418
45	4.7369	0.7501	1.5232	1.774	2.2192	3.0687	0.0916	0.5897	-0.8213	-0.6058	-0.0071	-0.7396	0.0703	0.0694	-0.0057	0.4809	0.0713	-0.0131	0.3801	-0.1054	0.3387	76.6154	-68.0723	30.6787
46	5.6731	-1.4573	-1.5063	2.4498	0.6726	1.9492	0.0164	0.5212	-1.5065	-0.7077	0.1902	0.1062	-0.2911	-0.6801	-0.1317	0.8811	0.1337	-0.1099	0.5094	-0.2492	0.6804	75.4089	-81.1763	30.6288
47	3.499	-0.3983	-1.535	5.1528	2.6515	1.7594	-0.148	0.5605	-0.4828	-1.1383	-0.1679	-0.0346	-0.613	-0.7735	0.2619	0.8611	0.0845	0.0277	0.576	-0.1766	0.7171	80.1811	-83.4841	27.562
48	0.7472	-0.1516	-0.7962	0.1354	0.4356	1.6613	0.1544	0.125	0.1679	-0.3869	-0.9117	-0.5914	0.6871	-0.1208	0.3708	1.0207	0.1122	0.1183	0.4322	-0.2143	0.8406	91.5938	-84.2756	31.1608
49	1.9973	0.0719	1.6551	4.2254	-0.0507	3.3973	0.4248	-0.4658	-1.3261	-0.1123	-0.1956	-0.3277	0.8295	0.072	-0.2234	0.53	0.0037	-0.1352	0.3548	0.1192	0.919	86.8543	-83.4206	51.3571
50	8.0053	-2.3453	2.0847	5.1517	-0.3062	4.3116	0.3739	0.0894	-1.0478	-0.3014	-0.1969	-0.8428	0.8229	0.3127	-0.1009	0.4507	0.0989	0.0124	0.2983	0.1194	0.8229	106.8331	-70.7182	49.8946
51	2.9097	0.3499	-0.6374	2.3444	0.7802	2.4015	0.0145	0.0437	-0.4662	-0.1553	-0.0983	-0.281	0.1674	0.0714	0.1167	0.2978	0.0805	0.0117	0.2827	0.0518	0.3995	99.4037	-59.5533	49.4533
52	7.7535	3.936	0.3818	5.4077	0.3848	2.509	-0.0341	-0.0735	-0.0567	-0.1813	0.0088	-0.1182	-0.0077	0.0867	0.0245	0.2827	0.0655	0.0037	0.2474	0.055	0.2376	97.5031	-49.6419	56.8535
53	3.7892	0.3923	-1.6571	3.1957	2.4739	8.0924	0.1253	-0.1484	0.1778	0.0783	-0.1652	-0.2166	-0.4541	0.1974	0.0299	0.3311	0.0344	-0.0297	0.3474	0.1359	0.3716	106.9745	-48.7806	62.8409
54	3.11	-0.129	-0.7921	3.1136	-0.3584	4.3429	-0.1633	0.11	-0.2796	-0.2774	-0.139	-0.7198	0.2275	0.7668	0.2919	0.3258	0.0855	0.1233	0.3986	0.0374	0.5695	110.7155	-58.1222	45.5251

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 5:87 )	A	5 - 87
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 88:127 )	A	88 - 127
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 128:165 )	A	128 - 165
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 166:197 )	A	166 - 197
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 198:217 )	A	198 - 217
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 4:37 )	B	4 - 37
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 38:87 )	B	38 - 87
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 88:101 )	B	88 - 101
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 102:120 )	B	102 - 120
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 121:165 )	B	121 - 165
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 166:179 )	B	166 - 179
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 180:217 )	B	180 - 217
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 4:37 )	C	4 - 37
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 38:85 )	C	38 - 85
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 86:102 )	C	86 - 102
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 113:127 )	C	113 - 127
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 128:152 )	C	128 - 152
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 153:179 )	C	153 - 179
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 180:197 )	C	180 - 197
20	X-RAY DIFFRACTION	20	( CHAIN C AND RESID 198:215 )	C	198 - 215
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 4:37 )	D	4 - 37
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 38:87 )	D	38 - 87
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 88:100 )	D	88 - 100
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 101:165 )	D	101 - 165
25	X-RAY DIFFRACTION	25	( CHAIN D AND RESID 166:197 )	D	166 - 197
26	X-RAY DIFFRACTION	26	( CHAIN D AND RESID 198:217 )	D	198 - 217
27	X-RAY DIFFRACTION	27	( CHAIN E AND RESID 3:17 )	E	3 - 17
28	X-RAY DIFFRACTION	28	( CHAIN E AND RESID 18:70 )	E	18 - 70
29	X-RAY DIFFRACTION	29	( CHAIN E AND RESID 71:116 )	E	71 - 116
30	X-RAY DIFFRACTION	30	( CHAIN E AND RESID 117:165 )	E	117 - 165
31	X-RAY DIFFRACTION	31	( CHAIN E AND RESID 166:217 )	E	166 - 217
32	X-RAY DIFFRACTION	32	( CHAIN F AND RESID 4:17 )	F	4 - 17
33	X-RAY DIFFRACTION	33	( CHAIN F AND RESID 18:70 )	F	18 - 70
34	X-RAY DIFFRACTION	34	( CHAIN F AND RESID 71:85 )	F	71 - 85
35	X-RAY DIFFRACTION	35	( CHAIN F AND RESID 86:102 )	F	86 - 102
36	X-RAY DIFFRACTION	36	( CHAIN F AND RESID 103:127 )	F	103 - 127
37	X-RAY DIFFRACTION	37	( CHAIN F AND RESID 128:139 )	F	128 - 139
38	X-RAY DIFFRACTION	38	( CHAIN F AND RESID 140:152 )	F	140 - 152
39	X-RAY DIFFRACTION	39	( CHAIN F AND RESID 153:165 )	F	153 - 165
40	X-RAY DIFFRACTION	40	( CHAIN F AND RESID 166:179 )	F	166 - 179
41	X-RAY DIFFRACTION	41	( CHAIN F AND RESID 180:217 )	F	180 - 217
42	X-RAY DIFFRACTION	42	( CHAIN G AND RESID 5:17 )	G	5 - 17
43	X-RAY DIFFRACTION	43	( CHAIN G AND RESID 18:56 )	G	18 - 56
44	X-RAY DIFFRACTION	44	( CHAIN G AND RESID 57:85 )	G	57 - 85
45	X-RAY DIFFRACTION	45	( CHAIN G AND RESID 86:102 )	G	86 - 102
46	X-RAY DIFFRACTION	46	( CHAIN G AND RESID 113:139 )	G	113 - 139
47	X-RAY DIFFRACTION	47	( CHAIN G AND RESID 140:165 )	G	140 - 165
48	X-RAY DIFFRACTION	48	( CHAIN G AND RESID 166:179 )	G	166 - 179
49	X-RAY DIFFRACTION	49	( CHAIN G AND RESID 180:217 )	G	180 - 217
50	X-RAY DIFFRACTION	50	( CHAIN H AND RESID 3:17 )	H	3 - 17
51	X-RAY DIFFRACTION	51	( CHAIN H AND RESID 18:70 )	H	18 - 70
52	X-RAY DIFFRACTION	52	( CHAIN H AND RESID 71:116 )	H	71 - 116
53	X-RAY DIFFRACTION	53	( CHAIN H AND RESID 117:165 )	H	117 - 165
54	X-RAY DIFFRACTION	54	( CHAIN H AND RESID 166:217 )	H	166 - 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