PDB-9br7: Crystal structure of human succinyl-CoA:glutarate-CoA transferase...

ID or keywords:

Entry

Database: PDB / ID: 9br7

Title

Crystal structure of human succinyl-CoA:glutarate-CoA transferase (SUGCT) in complex with Losartan carboxylic acid

Components

Succinate--hydroxymethylglutarate CoA-transferase

Keywords

TRANSFERASE / SUGCT / succinyl-CoA / glutarate

Function / homology

Function and homology information

succinate-hydroxymethylglutarate CoA-transferase / succinate-hydroxymethylglutarate CoA-transferase activity / Transferases; Transferring sulfur-containing groups; CoA-transferases / mitochondrion
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.08 Å

Authors

Wu, R. / Lazarus, M.B.

Funding support

United States, 1items

Citation

Journal: Acs Chem.Biol. / Year: 2024
Title: Characterization, Structure, and Inhibition of the Human Succinyl-CoA:glutarate-CoA Transferase, a Putative Genetic Modifier of Glutaric Aciduria Type 1.
Authors: Wu, R. / Khamrui, S. / Dodatko, T. / Leandro, J. / Sabovic, A. / Violante, S. / Cross, J.R. / Marsan, E. / Kumar, K. / DeVita, R.J. / Lazarus, M.B. / Houten, S.M.

History

Deposition	May 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9br7.cif.gz	633.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9br7.ent.gz		Display	PDB format
PDBx/mmJSON format	9br7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/br/9br7 ftp://data.pdbj.org/pub/pdb/validation_reports/br/9br7	HTTPS FTP

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Related structure data

Related structure data	9br6C C: citing same article (ref.)
Similar structure data	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	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Succinate--hydroxymethylglutarate CoA-transferase

B: Succinate--hydroxymethylglutarate CoA-transferase

C: Succinate--hydroxymethylglutarate CoA-transferase

D: Succinate--hydroxymethylglutarate CoA-transferase

hetero molecules

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

1

A: Succinate--hydroxymethylglutarate CoA-transferase

B: Succinate--hydroxymethylglutarate CoA-transferase

hetero molecules

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

2

C: Succinate--hydroxymethylglutarate CoA-transferase

D: Succinate--hydroxymethylglutarate CoA-transferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	107.933, 119.809, 136.246
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Succinate--hydroxymethylglutarate CoA-transferase / Dermal papilla-derived protein 13 / SuccinylCoA:glutarate-CoA transferase Mass: 44758.184 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUGCT, C7orf10, DERP13 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HAC7, succinate-hydroxymethylglutarate CoA-transferase
#2: Chemical	ChemComp-A1ATL / losartan carboxylic acid / 2-butyl-4-chloro-1-{[(2'M)-2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}-1H-imidazole-5-carboxylic acid / EXP3174 / E-3174 Mass: 436.894 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₂H₂₁ClN₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H₄N
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.920105 Å / Relative weight: 1
Reflection	Resolution: 2.08→34.31 Å / Num. obs: 106315 / % possible obs: 99.8 % / Redundancy: 4.8 % / CC_1/2: 0.997 / R_merge(I) obs: 0.134 / R_pim(I) all: 0.067 / R_rim(I) all: 0.15 / Χ²: 0.99 / Net I/σ(I): 6.8 / Num. measured all: 513724
Reflection shell	Resolution: 2.08→2.12 Å / % possible obs: 100 % / Redundancy: 5 % / R_merge(I) obs: 1.882 / Num. measured all: 26323 / Num. unique obs: 5254 / CC_1/2: 0.42 / R_pim(I) all: 0.923 / R_rim(I) all: 2.101 / Χ²: 1.02 / Net I/σ(I) obs: 0.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.08→34.06 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2473	5363	5.05 %
R_work	0.22	-	-
obs	0.2214	106147	99.72 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.08→34.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12346	0	130	218	12694

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002
X-RAY DIFFRACTION	f_angle_d	0.476
X-RAY DIFFRACTION	f_dihedral_angle_d	11.207	4682
X-RAY DIFFRACTION	f_chiral_restr	0.041	1924
X-RAY DIFFRACTION	f_plane_restr	0.003	2228

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 (%)
2.08-2.1	0.418	174	0.364	3345	X-RAY DIFFRACTION	100
2.1-2.13	0.3958	166	0.3447	3345	X-RAY DIFFRACTION	100
2.13-2.15	0.3241	180	0.3449	3330	X-RAY DIFFRACTION	100
2.15-2.18	0.3759	166	0.3302	3324	X-RAY DIFFRACTION	100
2.18-2.21	0.3621	162	0.3325	3350	X-RAY DIFFRACTION	100
2.21-2.24	0.4031	168	0.3243	3350	X-RAY DIFFRACTION	100
2.24-2.27	0.3526	169	0.33	3309	X-RAY DIFFRACTION	99
2.27-2.31	0.3944	190	0.3076	3321	X-RAY DIFFRACTION	100
2.31-2.34	0.3197	190	0.299	3318	X-RAY DIFFRACTION	100
2.34-2.38	0.3385	178	0.2904	3332	X-RAY DIFFRACTION	100
2.38-2.42	0.3404	182	0.287	3314	X-RAY DIFFRACTION	100
2.42-2.47	0.3185	168	0.2747	3350	X-RAY DIFFRACTION	100
2.47-2.51	0.2987	194	0.2676	3347	X-RAY DIFFRACTION	100
2.51-2.56	0.2798	184	0.2597	3325	X-RAY DIFFRACTION	100
2.56-2.62	0.3101	169	0.2505	3333	X-RAY DIFFRACTION	100
2.62-2.68	0.298	173	0.2502	3372	X-RAY DIFFRACTION	100
2.68-2.75	0.2781	186	0.2453	3335	X-RAY DIFFRACTION	100
2.75-2.82	0.2624	168	0.2466	3342	X-RAY DIFFRACTION	100
2.82-2.91	0.2955	189	0.2476	3348	X-RAY DIFFRACTION	100
2.91-3	0.2672	189	0.2483	3368	X-RAY DIFFRACTION	100
3-3.11	0.2842	204	0.2406	3326	X-RAY DIFFRACTION	100
3.11-3.23	0.2635	166	0.2388	3370	X-RAY DIFFRACTION	100
3.23-3.38	0.2423	182	0.2245	3362	X-RAY DIFFRACTION	100
3.38-3.56	0.2561	168	0.2118	3363	X-RAY DIFFRACTION	99
3.56-3.78	0.2022	178	0.1907	3379	X-RAY DIFFRACTION	99
3.78-4.07	0.2094	191	0.1757	3387	X-RAY DIFFRACTION	100
4.07-4.48	0.1673	168	0.161	3408	X-RAY DIFFRACTION	99
4.48-5.12	0.1809	169	0.1528	3402	X-RAY DIFFRACTION	99
5.12-6.45	0.1979	208	0.1897	3436	X-RAY DIFFRACTION	100
6.45-34.06	0.1916	184	0.1734	3593	X-RAY DIFFRACTION	99

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	5.5789	1.6509	0.305	3.2647	3.3431	5.9752	-0.3047	-0.9502	-0.3813	0.0059	0.4389	0.7999	0.3894	-1.0013	0.0144	0.7373	0.0564	0.0879	0.2641	0.0906	0.482	16.4143	-30.3176	-8.7271
2	2.5954	-0.9559	0.6249	0.7877	-0.9524	3.7965	-0.2873	-0.3283	0.1975	0.3859	0.185	0.1106	0.0149	-0.2384	0.036	0.5972	0.0769	0.0179	0.3151	-0.0068	0.2513	18.1934	-13.8524	2.1304
3	3.6765	-0.8853	1.9095	1.2908	-1.5654	5.0256	0.186	-0.5272	-0.2401	0.554	-0.0669	-0.06	-0.009	-0.3429	-0.0473	0.7561	0.0393	-0.0006	0.3326	0.0296	0.322	25.7949	-23.4701	14.1282
4	2.3226	-0.182	0.7486	1.4199	-1.2544	3.6578	0.1081	-0.312	-0.1868	0.1729	-0.1933	-0.1151	0.7234	0.2279	0.0954	0.7293	0.1439	-0.0168	0.3624	0.0234	0.3133	32.4156	-22.7788	5.52
5	9.7682	1.2029	-0.7647	1.9894	3.0471	5.1909	-0.0035	-1.1721	-1.0787	0.7338	0.3163	-1.2107	0.7304	2.3816	-0.2492	0.9173	0.1936	-0.0566	0.775	0.1615	0.5805	38.7069	-28.898	5.5482
6	1.1574	-0.3369	0.1094	1.5954	0.595	2.2923	-0.1662	-0.1054	0.0003	0.3369	0.038	-0.0134	-0.2461	0.2201	0.0954	0.5929	0.1013	0.0046	0.3191	0.005	0.2199	32.1864	-8.3533	-7.0858
7	3.8733	-2.4035	1.5942	8.4901	-2.9825	1.5654	-0.4584	-0.2459	0.6519	0.1292	-0.2271	-0.2712	-0.2602	-0.3194	0.1541	1.3432	0.5631	0.3383	0.0805	0.1623	0.9193	32.9135	-34.4466	-11.3341
8	2.1997	-0.1426	-0.5153	4.6595	2.009	1.0822	-0.0084	0.0626	-0.0718	-0.5744	-0.0325	-0.1462	0.485	0.3971	0.0592	0.373	0.1218	-0.0017	0.3008	-0.0217	0.2459	37.6604	-10.0719	-14.3466
9	1.0966	1.0382	-0.1129	1.0101	0.3731	4.7306	0.3193	0.1863	0.3272	-0.8692	-0.2013	0.5079	-1.2519	0.5103	-0.0097	0.8936	-0.0076	0.0398	0.5205	0.1159	0.5483	38.121	7.8287	-20.6259
10	3.1557	1.3731	0.4622	1.0015	-0.3833	3.9569	-0.0042	0.1948	-0.021	-0.2141	-0.2006	0.0258	-0.2221	-0.0083	0.1547	0.6704	0.1273	-0.0509	0.298	-0.0038	0.3239	19.5632	9.2302	-31.3094
11	2.0092	-2.0743	-7.0887	5.0695	2.8713	5.2784	-0.7163	1.6384	0.1388	-0.586	-0.335	0.7724	-0.595	-1.144	-0.1455	1.6137	0.0359	-0.1432	0.4381	0.104	0.1764	17.412	16.4538	-43.0208
12	5.4764	1.7048	-2.4817	2.414	-0.3834	2.1432	0.1074	0.0919	0.3767	-0.0095	-0.114	0.0526	-0.7396	0.0048	-0.004	0.8668	0.1214	-0.1283	0.3748	0.0067	0.2772	18.6666	14.3618	-33.9594
13	0.5931	0.9864	0.4168	2.5642	-1.3559	2.7907	-0.0127	0.0002	-0.0603	0.0465	0.0569	0.1123	-0.0613	-0.2967	-0.0464	0.5822	0.172	-0.0309	0.3689	-0.0511	0.3342	8.7588	-1.956	-21.2864
14	0.8351	1.1035	-0.7231	1.6158	-1.5998	6.5227	0.1099	-0.3227	-0.5022	0.7228	-0.1446	0.3837	0.4962	-0.0163	-0.3012	0.7982	0.0173	0.076	0.6084	-0.0106	0.566	4.4103	-14.3143	-5.5597
15	1.4579	-2.0568	-0.7733	5.1307	-3.0561	9.8142	-0.1144	-0.5728	0.1016	0.3254	-0.0754	0.3653	0.1506	-1.6449	-0.09	0.8451	0.0484	0.151	0.7321	0.01	0.5755	2.7042	-14.1292	3.9867
16	1.0385	-0.2191	0.1192	1.6737	0.4632	5.7594	0.1931	-0.0482	-0.3436	-0.6227	-0.355	0.5709	-0.6363	-0.985	-0.1443	0.5454	0.0418	0.0433	0.37	0.0141	0.3805	11.4847	-15.8762	-13.2909
17	3.0544	-0.2502	1.3558	3.7428	0.782	6.531	-0.9043	-0.1571	-0.6821	0.1642	0.9816	0.5531	0.5616	-0.2791	-0.1797	0.5986	0.0009	-0.0457	0.4176	0.0456	0.4395	9.3597	-24.1692	-14.0699
18	1.343	-0.4769	1.7182	1.5899	-0.6181	7.5127	0.1665	-0.3745	-0.3994	0.1828	0.374	0.4158	0.8467	-0.7882	-0.2006	0.6607	-0.0332	0.0407	0.3694	0.0184	0.2865	11.9222	-20.8357	6.5487
19	7.8635	1.8979	1.0516	1.6253	1.2311	1.3578	-0.2997	-0.6931	-1.5796	0.2777	0.3279	-0.4153	0.8144	-1.1787	-0.0304	1.125	0.0431	0.1239	0.6324	0.1591	0.629	17.6568	-32.9309	15.8811
20	6.549	-0.529	4.9032	2.2828	-2.345	5.9708	-0.7224	-0.6499	0.4145	0.5615	0.1322	0.3144	-0.553	-1.1007	-0.0055	0.9947	0.0215	0.0475	0.5324	-0.0164	0.2962	13.7498	-21.8112	17.4942
21	8.1752	-6.3447	-1.8025	6.2859	3.0816	6.0822	0.2861	-1.3058	-0.6482	0.8849	-0.4058	-2.4322	1.512	1.907	0.7337	1.327	0.1274	0.137	0.619	0.181	0.7988	46.4269	-30.9428	-17.297
22	2.4903	0.1235	1.1884	6.1094	1.2606	4.642	-0.0314	0.1749	0.0098	-0.7117	0.0529	-0.2853	0.287	0.2918	-0.0143	0.5216	0.0464	0.0865	0.3085	0.0045	0.2823	31.7429	-20.0929	-25.008
23	3.8883	0.4486	1.5246	6.1491	-4.3678	4.7648	0.0984	0.4418	0.495	-0.9392	-0.704	-0.9325	0.9983	0.2473	0.7184	0.8194	0.1952	0.0652	0.3959	0.0139	0.3263	31.8276	-19.6675	-35.1597
24	2.3729	1.7757	1.3211	1.9906	1.3567	3.184	-0.2041	0.2455	0.015	-0.3783	0.1302	0.0702	-0.1179	0.2326	0.062	0.6269	0.1029	0.0618	0.2991	0.008	0.2951	31.4072	-16.1332	-35.8862
25	3.1562	0.204	1.5799	1.1451	1.8356	4.9325	-0.3095	0.2913	0.0767	-0.6272	0.0759	0.0141	0.4752	-0.0705	0.3068	0.6505	0.0734	-0.0376	0.3601	-0.0506	0.3085	16.1332	-18.8706	-36.4996
26	2.1108	-0.7879	-1.9536	3.917	2.3847	6.4076	-0.0227	0.1528	-0.2136	-0.6467	-0.5615	0.3724	0.1762	-1.0168	0.2759	0.7979	-0.047	0.0429	0.3792	-0.0579	0.3592	17.9621	-29.1424	-31.3479
27	1.0815	-0.0437	0.0872	2.1814	0.1603	1.4565	-0.0739	0.0881	0.1424	-0.2485	-0.0685	0.0827	-0.3972	-0.2919	0.1238	0.6384	0.1208	0.0023	0.3209	0.0061	0.2586	19.4142	-5.7038	-20.4446
28	5.7387	-0.5186	-1.4284	8.2847	1.6682	7.4754	-0.2782	0.147	1.1716	-0.3665	0.5968	-1.1845	0.2916	0.5167	0.1404	0.9022	-0.0288	0.0708	0.2552	-0.0071	0.5019	20.2179	-35.1023	-18.9242
29	0.4222	-0.5459	-0.085	3.2632	-0.1987	2.2695	-0.1272	-0.0676	0.0259	0.6015	-0.0827	-0.0044	0.2399	-0.5477	0.117	0.4349	0.1096	-0.0213	0.363	-0.0302	0.2798	13.7638	-9.2641	-13.8717
30	0.689	0.0054	-0.7025	1.0987	-1.5162	4.9611	-0.6939	0.1113	-0.0914	-0.2293	0.2247	-0.4277	-1.251	-1.1047	0.4985	0.9823	0.1859	-0.014	0.5012	-0.0561	0.4793	11.783	6.4791	-7.505
31	2.3009	-0.5408	-0.3155	2.5867	0.2444	2.3871	-0.0934	-0.2016	0.0757	0.2679	-0.0252	0.0525	0.0404	-0.0416	0.1058	0.7107	0.0866	-0.0467	0.3199	-0.025	0.2799	29.9432	10.338	6.6214
32	9.0086	-0.9734	-3.5838	0.7207	0.2365	2.8191	0.0811	-0.0652	0.5803	0.0257	0.0159	-0.0087	-0.3522	-0.1624	-0.1263	0.7637	0.0786	-0.0863	0.3342	-0.0508	0.289	32.2674	14.6361	4.2916
33	2.0263	-2.6835	-1.3195	6.2728	0.8969	2.4626	-0.5447	-0.4824	-0.3804	0.502	0.5492	-0.7763	-0.1237	1.0353	0.5251	0.7533	0.1837	0.0081	0.5241	0.0681	0.3648	40.5976	3.2985	6.9829
34	3.7318	-1.7194	-1.3911	2.3272	1.8167	4.7671	-0.2248	0.1247	-0.0593	0.2843	0.0661	-0.0447	-0.1431	0.5375	0.212	0.4761	0.0236	0.0059	0.3265	0.0018	0.2703	43.1705	-1.8951	-10.1632
35	7.7828	-1.6088	-2.0254	6.931	4.182	8.069	-0.0347	-0.3825	-0.0845	0.1012	1.0788	-1.0786	-0.4284	1.4436	-0.9102	0.7833	-0.0179	0.0399	0.59	-0.0908	0.5129	48.8753	-11.7808	-30.0428
36	3.1392	1.4228	-1.8979	5.5163	-2.0762	4.8514	0.3259	-0.1654	0.2318	0.3868	-0.1945	-0.0037	-0.644	-0.0235	-0.2809	0.565	0.0678	-0.0656	0.2924	0.0116	0.3448	40.4854	-11.5129	-17.8399
37	4.201	0.7925	0.1247	4.3152	-0.1826	3.0396	-0.4433	-0.3178	-0.2197	0.9386	0.3612	-0.509	-0.3271	0.8573	-0.0843	0.782	0.1974	-0.0628	0.4123	-0.0042	0.3072	42.4623	-22.0211	-13.0073
38	5.626	3.8991	1.2248	7.5659	3.6854	4.4349	0.1093	-0.0626	-0.9006	0.3651	0.2789	-0.9684	0.8697	0.4291	-0.2909	0.6164	0.1867	0.0481	0.3807	0.0462	0.3495	38.9615	-24.6571	-37.1558
39	7.161	0.1425	1.434	4.526	1.0417	1.8619	-0.2496	0.7818	-0.7139	-0.8501	0.0095	-0.5085	0.5902	0.4767	0.2363	0.9629	0.1494	0.1324	0.4363	-0.057	0.396	34.971	-27.9783	-49.9584
40	9.5115	1.2	6.378	9.6929	3.4892	5.0841	-0.4308	1.1851	-0.4532	-0.2327	0.9699	-1.194	-0.433	1.3782	-0.3284	0.7694	0.1387	0.0967	0.605	-0.0433	0.3848	44.1426	-18.8862	-43.2823
41	9.7078	-1.3217	-0.2651	0.4521	0.4088	3.1202	0.4763	0.4788	-0.7287	-0.8708	-0.4659	1.3615	2.1508	-1.4782	-0.2974	1.0845	-0.2023	-0.1427	0.6409	-0.0869	0.4789	2.2221	-71.3036	-29.4572
42	3.9293	-0.9	0.2116	2.6369	0.8257	2.7775	-0.0326	0.1903	0.0401	-0.2756	0.0621	-0.1111	0.4702	-0.1651	0.1911	0.7021	-0.1787	0.0583	0.3727	-0.0185	0.2895	14.1802	-61.0691	-31.7663
43	1.1156	-2.2931	0.5664	7.0741	1.9101	3.988	0.4766	-0.1769	-0.1087	-0.8551	-0.2461	-0.9784	0.2354	0.8072	0.2094	0.3527	-0.2277	0.0605	0.5422	-0.0841	0.4629	16.7153	-55.8416	-41.6168
44	1.6897	-0.876	-0.2506	2.6479	0.2312	2.591	0.1703	0.2722	0.2978	-0.0382	0.0514	-0.3188	0.3634	0.3621	-0.2244	0.6821	-0.1615	0.0371	0.4675	-0.0495	0.3873	23.647	-63.8519	-40.8218
45	3.3101	0.2349	-1.7528	4.9022	-0.2022	5.6159	0.0333	0.8697	0.4474	-0.6484	0.2435	-0.1878	-1.1256	-0.8433	0.0042	0.6812	-0.2013	0.0378	0.391	0.0237	0.3433	10.8691	-45.5233	-43.3644
46	0.8276	-0.717	0.7233	2.6298	0.9012	2.8256	-0.2507	0.0356	0.1863	-0.3496	0.2361	-0.1472	-0.072	-0.2629	-0.0439	0.5174	-0.1053	0.0062	0.3152	-0.01	0.2649	13.7562	-47.4271	-32.1605
47	5.2439	-1.9009	-5.4929	6.0968	1.4223	5.804	0.3995	-0.1507	0.9291	1.022	-0.2726	-0.6926	-2.2502	-0.9477	0.0165	1.0001	-0.0777	-0.0601	0.5993	-0.0564	0.4499	5.7458	-42.4228	-30.5656
48	1.3519	-1.1734	-0.0213	0.5805	-0.6146	0.9239	0.0798	0.1525	-0.0667	0.0762	-0.0815	-0.2317	0.2325	0.0713	0.0785	0.5165	-0.1172	-0.0088	0.3249	0.0004	0.3571	26.6799	-51.5976	-21.8604
49	3.2643	-0.9673	-0.0307	1.2832	-0.2583	1.2015	-0.131	0.0313	-0.2614	0.1874	-0.0621	-0.1491	0.0379	0.0166	0.1205	0.6526	-0.1498	0.006	0.3039	0.0239	0.3589	25.4103	-61.7226	-20.5403
50	7.9478	-1.3428	1.2286	2.8724	-4.0448	8.0083	0.5936	-0.0915	0.0672	-0.4115	0.7763	-0.2419	0.2563	-0.3222	-0.0108	0.4949	-0.1048	-0.0252	0.8073	-0.0684	0.4613	-0.743	-53.4133	-19.8676
51	3.8651	-0.2862	0.5368	0.4096	-0.8534	1.7927	-0.4225	-0.0011	-0.1207	0.3124	0.1235	0.0694	-0.2368	0.2766	0.3202	0.5448	-0.0744	-0.0395	0.2465	-0.016	0.3357	25.0744	-55.0179	-11.9491
52	0.2297	-0.1372	0.819	0.4208	0.08	6.0275	0.4337	-0.6831	0.4975	-1.3063	0.6261	-1.0241	-1.9434	0.1284	-0.7656	0.7844	-0.0945	0.0666	0.5689	-0.1256	0.6037	39.5125	-58.2134	-3.7573
53	3.1692	1.0715	0.9742	5.3874	-0.361	2.4418	0.5961	-0.024	-0.3185	0.6952	-0.4856	-0.0716	0.4208	0.1261	-0.1392	1.0686	-0.0073	-0.0775	0.3941	-0.0288	0.4763	39.4581	-80.1954	-7.3834
54	5.4179	3.2968	0.8572	4.276	2.3859	1.799	0.7026	-0.681	-0.6624	0.2945	-0.5115	-0.4513	1.5122	0.3068	0.0494	1.3382	-0.056	-0.2159	0.553	-0.0161	0.6552	43.5929	-81.7221	3.7242
55	3.5401	1.8023	2.1769	3.0007	3.3327	7.1848	0.0361	0.1927	-0.5314	-0.1105	0.0289	-0.7913	1.1124	0.467	-0.0376	0.9963	0.1164	-0.12	0.4919	0.0293	0.7798	44.5493	-87.3261	-10.6887
56	1.2491	0.1005	0.8531	1.5942	-0.3292	1.3714	0.0544	0.1539	-0.2224	0.0518	-0.0475	-0.1305	1.0607	-0.0428	-0.0841	1.0195	-0.0462	-0.0148	0.3741	-0.0521	0.4941	28.2735	-83.1528	-23.0203
57	2.0595	-0.372	-0.2875	1.3156	-1.8678	6.2001	0.2528	0.1087	-0.3913	-0.3003	0.0498	0.4589	0.9556	-0.3626	-0.0644	0.9755	-0.0563	-0.0086	0.5787	-0.0862	0.5347	18.6047	-75.3303	-44.7198
58	0.9814	0.1442	0.194	0.1627	-0.2969	1.6733	0.0541	0.0716	-0.1621	-0.1674	-0.0427	0.0811	0.6429	-0.0772	-0.058	0.838	-0.1596	0.0088	0.4252	-0.0691	0.4459	13.1036	-71.2846	-34.9549
59	2.6821	0.129	-0.7646	5.2766	-1.0372	2.2407	0.3316	0.3579	-0.4615	-0.7793	-0.2324	0.4239	-0.5825	0.3964	-0.1867	0.9002	-0.1887	-0.0475	0.4717	-0.0004	0.3668	2.4106	-53.8519	-50.5748
60	5.8704	-4.4814	2.0655	7.8685	-3.7196	4.7236	0.6162	0.2396	0.1464	-0.9072	-0.4456	-0.9607	0.0337	0.3632	-0.2657	0.8609	-0.2615	0.0312	0.5875	0.0288	0.3134	13.2735	-55.7943	-53.0334
61	2.2863	0.9219	-2.0847	1.7079	-3.4182	7.8275	0.3988	0.1599	1.0805	0.961	0.1666	0.4937	-2.5301	-1.1508	-0.5087	0.8284	-0.0495	0.0536	0.5611	-0.0339	0.5045	3.8036	-53.8682	-10.2632
62	7.2393	-2.2541	0.4906	3.6803	1.5832	1.6507	-0.4282	-0.3165	-0.0993	0.7237	0.2966	-0.1278	0.0083	-0.0747	0.1271	0.7145	-0.0937	-0.0029	0.3376	0.0351	0.3026	12.7851	-65.6123	-6.5325
63	3.9617	2.7373	-0.2446	4.1797	-0.7134	5.7752	-0.1468	-0.6344	-0.2471	-0.0086	-0.068	-1.455	0.7161	0.3403	-0.0179	0.8355	-0.1011	0.0539	0.4455	-0.0301	0.4541	13.0504	-71.8917	2.5786
64	6.3151	2.1659	-1.2269	1.9991	-0.0579	2.5032	0.4602	-0.6613	-2.1846	-0.2193	-0.177	-0.1767	0.1863	0.4204	0.1755	0.9566	-0.1081	-0.124	0.5658	0.206	0.5676	22.7821	-71.653	4.3455
65	1.8378	0.6665	0.7791	1.6657	0.4931	0.6804	0.6201	-1.1376	-0.1094	1.251	-0.0686	-0.3042	-0.2827	-0.4273	0.0937	1.1001	-0.0706	-0.0409	0.5681	-0.0096	0.4225	28.8376	-63.0671	7.6165
66	4.3644	1.3975	-0.039	1.8	-0.7275	2.634	0.0052	-0.1363	-0.5946	-0.0831	-0.0852	-0.3082	0.0802	0.1035	0.0293	0.7488	-0.1243	-0.0427	0.4043	0.0012	0.3315	17.32	-65.9131	1.3596
67	5.3899	0.1333	2.1176	3.9739	-2.1607	4.4117	-0.0201	-0.6693	-0.6839	0.7063	0.3446	0.0532	0.3061	-0.6791	-0.1	0.8418	-0.1834	-0.0128	0.4451	0.0442	0.4488	2.9782	-78.1642	2.7338
68	2.6053	-1.1463	-0.6245	0.4209	0.0131	1.0563	-0.2516	-0.2071	-0.2803	0.1931	0.1149	0.096	0.5397	-0.1388	0.1879	0.9447	-0.1757	0.0441	0.3416	-0.0359	0.4351	16.1316	-79.1939	-12.2042
69	5.8244	-1.4497	-1.9873	1.8012	0.8955	3.2002	-0.4379	-0.1934	-0.2643	-0.1173	0.1707	-0.4033	0.8191	0.5755	0.1938	0.8382	0.0236	0.0487	0.4158	0.0915	0.5623	41.6669	-69.4889	-18.9842
70	2.9733	-1.1256	-0.0605	0.1763	-0.3684	1.9037	-0.2818	0.1162	-0.1243	0.0363	0.1127	0.0369	0.3302	-0.1131	0.1595	0.7488	-0.1802	0.0321	0.3329	-0.031	0.3975	16.474	-71.0254	-21.5704
71	1.6668	2.008	2.2406	3.0219	4.4367	9.6765	0.3247	0.8636	-1.6661	0.1926	0.4122	-1.2065	0.702	1.5342	-0.5165	0.6563	0.0942	-0.0566	0.588	-0.1606	0.6696	40.0832	-72.358	-31.0188
72	4.1338	0.8622	0.4474	7.1881	-0.0626	4.0924	-0.2075	0.3209	0.1005	-0.8423	0.1494	-0.3156	-0.0693	0.337	0.1154	0.7053	-0.188	0.0274	0.4461	0.0023	0.4282	43.038	-53.8613	-28.2815
73	5.39	0.0215	-1.5468	4.8965	-1.7203	7.1601	-0.4923	0.8334	-0.3343	-0.9791	0.2482	-0.5838	-0.3672	1.058	0.3806	0.6288	-0.2381	0.0726	0.8016	-0.0547	0.552	49.2451	-51.2587	-36.7407
74	8.7307	0.7667	1.3371	2.6236	-1.4153	6.9753	-0.0322	-0.372	1.2344	0.6134	-0.6349	-0.8788	-1.4104	0.4858	0.4645	0.4919	-0.2419	-0.0336	0.5436	0.0589	0.572	47.141	-43.072	-21.8771
75	2.3405	-0.8281	-1.6403	2.044	1.3028	2.0637	-0.211	-0.0724	0.3975	0.0627	0.203	-0.168	-0.072	0.2518	-0.0429	0.5931	-0.1433	-0.0689	0.3553	0.0002	0.3907	32.6432	-48.0277	-14.3634
76	3.9105	-0.0018	0.4	2.2629	-2.3568	9.5172	0.0768	-0.2229	0.6092	0.2408	0.0473	0.4615	-0.8571	-0.0536	0.1055	0.8271	-0.1636	-0.0053	0.4779	-0.1152	0.436	20.545	-53.0272	6.2905
77	5.3713	-1.5184	3.2205	1.539	-0.1927	4.7403	0.4532	-0.6059	0.0999	-0.19	-0.06	-0.229	-0.5416	0.0856	-0.1874	0.6235	-0.1418	0.0313	0.3174	-0.0275	0.3272	15.3838	-51.0001	-11.8234
78	3.0096	2.0938	-1.8221	1.8121	-2.9201	5.7488	0.0614	-0.3366	0.2827	-0.0644	0.184	0.43	-0.319	-0.2931	-0.2899	0.7739	-0.1116	0.014	0.4241	-0.0466	0.3069	11.2943	-60.8133	5.076
79	3.5289	0.0251	1.1365	4.0134	-0.4907	6.2444	0.8423	-0.8708	0.9476	0.0717	-0.1308	0.5251	-0.3153	-0.2959	-0.3863	0.8986	-0.192	0.0055	0.5094	0.0205	0.4559	-2.7972	-68.8013	10.7173
80	6.7497	-0.0704	-1.6116	4.5022	-3.0406	3.2243	0.682	-1.022	-0.1766	0.9312	-0.571	0.0886	-0.492	0.2884	-0.13	0.8381	-0.1609	-0.0896	0.5813	0.0671	0.3492	7.8812	-70.9592	14.9764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 37 : 45 )
2	X-RAY DIFFRACTION	2	(chain A and resid 46 : 103 )
3	X-RAY DIFFRACTION	3	(chain A and resid 104 : 119 )
4	X-RAY DIFFRACTION	4	(chain A and resid 120 : 145 )
5	X-RAY DIFFRACTION	5	(chain A and resid 146 : 150 )
6	X-RAY DIFFRACTION	6	(chain A and resid 151 : 221 )
7	X-RAY DIFFRACTION	7	(chain A and resid 222 : 226 )
8	X-RAY DIFFRACTION	8	(chain A and resid 227 : 254 )
9	X-RAY DIFFRACTION	9	(chain A and resid 255 : 260 )
10	X-RAY DIFFRACTION	10	(chain A and resid 261 : 298 )
11	X-RAY DIFFRACTION	11	(chain A and resid 299 : 305 )
12	X-RAY DIFFRACTION	12	(chain A and resid 306 : 343 )
13	X-RAY DIFFRACTION	13	(chain A and resid 344 : 369 )
14	X-RAY DIFFRACTION	14	(chain A and resid 370 : 374 )
15	X-RAY DIFFRACTION	15	(chain A and resid 375 : 380 )
16	X-RAY DIFFRACTION	16	(chain A and resid 381 : 391 )
17	X-RAY DIFFRACTION	17	(chain A and resid 392 : 397 )
18	X-RAY DIFFRACTION	18	(chain A and resid 398 : 409 )
19	X-RAY DIFFRACTION	19	(chain A and resid 410 : 426 )
20	X-RAY DIFFRACTION	20	(chain A and resid 427 : 438 )
21	X-RAY DIFFRACTION	21	(chain B and resid 34 : 38 )
22	X-RAY DIFFRACTION	22	(chain B and resid 39 : 67 )
23	X-RAY DIFFRACTION	23	(chain B and resid 68 : 74 )
24	X-RAY DIFFRACTION	24	(chain B and resid 75 : 132 )
25	X-RAY DIFFRACTION	25	(chain B and resid 133 : 145 )
26	X-RAY DIFFRACTION	26	(chain B and resid 146 : 158 )
27	X-RAY DIFFRACTION	27	(chain B and resid 159 : 221 )
28	X-RAY DIFFRACTION	28	(chain B and resid 222 : 228 )
29	X-RAY DIFFRACTION	29	(chain B and resid 229 : 254 )
30	X-RAY DIFFRACTION	30	(chain B and resid 255 : 260 )
31	X-RAY DIFFRACTION	31	(chain B and resid 261 : 312 )
32	X-RAY DIFFRACTION	32	(chain B and resid 313 : 341 )
33	X-RAY DIFFRACTION	33	(chain B and resid 342 : 347 )
34	X-RAY DIFFRACTION	34	(chain B and resid 348 : 371 )
35	X-RAY DIFFRACTION	35	(chain B and resid 372 : 381 )
36	X-RAY DIFFRACTION	36	(chain B and resid 382 : 388 )
37	X-RAY DIFFRACTION	37	(chain B and resid 389 : 397 )
38	X-RAY DIFFRACTION	38	(chain B and resid 398 : 417 )
39	X-RAY DIFFRACTION	39	(chain B and resid 418 : 433 )
40	X-RAY DIFFRACTION	40	(chain B and resid 434 : 438 )
41	X-RAY DIFFRACTION	41	(chain C and resid 36 : 42 )
42	X-RAY DIFFRACTION	42	(chain C and resid 43 : 68 )
43	X-RAY DIFFRACTION	43	(chain C and resid 69 : 76 )
44	X-RAY DIFFRACTION	44	(chain C and resid 77 : 107 )
45	X-RAY DIFFRACTION	45	(chain C and resid 108 : 122 )
46	X-RAY DIFFRACTION	46	(chain C and resid 123 : 145 )
47	X-RAY DIFFRACTION	47	(chain C and resid 146 : 152 )
48	X-RAY DIFFRACTION	48	(chain C and resid 153 : 191 )
49	X-RAY DIFFRACTION	49	(chain C and resid 192 : 221 )
50	X-RAY DIFFRACTION	50	(chain C and resid 222 : 228 )
51	X-RAY DIFFRACTION	51	(chain C and resid 229 : 254 )
52	X-RAY DIFFRACTION	52	(chain C and resid 255 : 259 )
53	X-RAY DIFFRACTION	53	(chain C and resid 260 : 297 )
54	X-RAY DIFFRACTION	54	(chain C and resid 298 : 319 )
55	X-RAY DIFFRACTION	55	(chain C and resid 320 : 343 )
56	X-RAY DIFFRACTION	56	(chain C and resid 344 : 371 )
57	X-RAY DIFFRACTION	57	(chain C and resid 372 : 380 )
58	X-RAY DIFFRACTION	58	(chain C and resid 381 : 409 )
59	X-RAY DIFFRACTION	59	(chain C and resid 410 : 425 )
60	X-RAY DIFFRACTION	60	(chain C and resid 426 : 438 )
61	X-RAY DIFFRACTION	61	(chain D and resid 37 : 42 )
62	X-RAY DIFFRACTION	62	(chain D and resid 43 : 69 )
63	X-RAY DIFFRACTION	63	(chain D and resid 70 : 74 )
64	X-RAY DIFFRACTION	64	(chain D and resid 75 : 84 )
65	X-RAY DIFFRACTION	65	(chain D and resid 85 : 92 )
66	X-RAY DIFFRACTION	66	(chain D and resid 93 : 110 )
67	X-RAY DIFFRACTION	67	(chain D and resid 111 : 126 )
68	X-RAY DIFFRACTION	68	(chain D and resid 127 : 190 )
69	X-RAY DIFFRACTION	69	(chain D and resid 191 : 201 )
70	X-RAY DIFFRACTION	70	(chain D and resid 202 : 254 )
71	X-RAY DIFFRACTION	71	(chain D and resid 255 : 261 )
72	X-RAY DIFFRACTION	72	(chain D and resid 262 : 290 )
73	X-RAY DIFFRACTION	73	(chain D and resid 291 : 330 )
74	X-RAY DIFFRACTION	74	(chain D and resid 331 : 343 )
75	X-RAY DIFFRACTION	75	(chain D and resid 344 : 371 )
76	X-RAY DIFFRACTION	76	(chain D and resid 372 : 381 )
77	X-RAY DIFFRACTION	77	(chain D and resid 382 : 395 )
78	X-RAY DIFFRACTION	78	(chain D and resid 396 : 411 )
79	X-RAY DIFFRACTION	79	(chain D and resid 412 : 421 )
80	X-RAY DIFFRACTION	80	(chain D and resid 422 : 438 )

-
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

+
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