PDB-6fl3: Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in...

ID or keywords:

Entry

Database: PDB / ID: 6fl3

Title

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase from A. thaliana in complex with myo-IP5 and ADP

Components

Inositol-pentakisphosphate 2-kinase

Keywords

TRANSFERASE / IPK1 / MYO-IP5

Function / homology

Function and homology information

inositol tetrakisphosphate 2-kinase activity /

inositol-pentakisphosphate 2-kinase / inositol pentakisphosphate 2-kinase activity / myo-inositol hexakisphosphate biosynthetic process / lateral root development / intracellular phosphate ion homeostasis / phosphate ion homeostasis / defense response to fungus / defense response to virus / defense response to bacterium ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.36 Å

Authors

Whitfield, H.L. / Brearley, C.A. / Hemmings, A.M.

Citation

Journal: J. Med. Chem. / Year: 2018
Title: A Fluorescent Probe Identifies Active Site Ligands of Inositol Pentakisphosphate 2-Kinase.
Authors: Whitfield, H. / Gilmartin, M. / Baker, K. / Riley, A.M. / Godage, H.Y. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A.

History

Deposition	Jan 25, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 31, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Jan 17, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6fl3.cif.gz	355.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6fl3.ent.gz	285.6 KB	Display	PDB format
PDBx/mmJSON format	6fl3.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/fl/6fl3 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/6fl3	HTTPS FTP

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Related structure data

Related structure data	6fjkC 6fl8C 6gfgC 6gfhC 2xamS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fjk-1 6fjk-2 5xv4-2 5xv4-3 5xv3-1 5xuy-1 6gfh-2 5xv4-5 6gfh-1 5xv3-2 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

Deposited unit

A: Inositol-pentakisphosphate 2-kinase

B: Inositol-pentakisphosphate 2-kinase

hetero molecules

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

1

A: Inositol-pentakisphosphate 2-kinase

hetero molecules

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

2

B: Inositol-pentakisphosphate 2-kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.950, 59.010, 83.360
Angle α, β, γ (deg.)	88.980, 89.560, 63.650
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 2 molecules AB

#1: Protein	Inositol-pentakisphosphate 2-kinase / Mass: 52863.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXX17_At5g40720 / Production host: Escherichia coli (E. coli) References: UniProt: A0A178UAB5, UniProt: Q93YN9*PLUS, inositol-pentakisphosphate 2-kinase

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Non-polymers , 6 types, 426 molecules

#2: Chemical	ChemComp-5MY / MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE Mass: 580.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₇O₂₁P₅
#3: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.46 Å³/Da / Density % sol: 49.95 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18 % PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2, 25% EG or 35% PEG 3350, 0.1 M bis-tris propane pH 6.5, 2 mM MgCl2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.9173 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9173 Å / Relative weight: 1

Reflection

Resolution: 2.36→52.872 Å / Num. obs: 37982 / % possible obs: 91.8 % / Redundancy: 2.1 % / B_iso Wilson estimate: 32.59 Å² / R_pim(I) all: 0.069 / R_rim(I) all: 0.103 / R_sym value: 0.074 / Net I/av σ(I): 9.4 / Net I/σ(I): 8.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
2.36-2.42	2.2	0.408	1.9	2806	0.36	0.535	0.408	93.5
2.42-2.49	2.2	0.351	2.2	2821	0.307	0.457	0.351	93.8
2.49-2.56	2.2	0.26	3	2712	0.267	0.396	0.26	93.1
2.56-2.64	2.2	0.247	3.1	2603	0.237	0.352	0.247	92.9
2.64-2.73	2.2	0.214	3.6	2535	0.203	0.3	0.214	92.6
2.73-2.82	2.2	0.19	4.1	2463	0.161	0.239	0.19	92.4
2.82-2.93	2.2	0.158	4.9	2314	0.141	0.21	0.158	91.1
2.93-3.05	2.2	0.139	5.5	2209	0.119	0.177	0.139	90.8
3.05-3.18	2.1	0.101	7.6	2058	0.096	0.143	0.101	87.4
3.18-3.34	2.1	0.075	10	1832	0.077	0.115	0.075	80.7
3.34-3.52	2.1	0.067	11.8	1980	0.064	0.095	0.067	92.9
3.52-3.73	2.2	0.054	13.5	1918	0.05	0.075	0.054	94.6
3.73-3.99	2.1	0.048	15.7	1807	0.046	0.068	0.048	95.1
3.99-4.31	2.2	0.043	17.5	1661	0.042	0.063	0.043	94.7
4.31-4.72	2.1	0.04	17	1511	0.039	0.057	0.04	93.3
4.72-5.28	2.1	0.043	16.5	1387	0.042	0.062	0.043	92.3
5.28-6.09	2.1	0.046	15.2	1132	0.042	0.062	0.046	88
6.09-7.46	2.1	0.037	19	948	0.038	0.057	0.037	85.9
7.46-10.55	2.2	0.033	20.7	828	0.03	0.045	0.033	98.6
10.55-52.872	2.2	0.035	18.2	457	0.029	0.043	0.035	97.5

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Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2XAM

2xam

Resolution: 2.36→52.872 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 23.7

	R_factor	Num. reflection	% reflection
R_free	0.2173	1898	5 %
R_work	0.1543	-	-
obs	0.1575	37980	91.83 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 147.02 Å² / B_iso mean: 38.5816 Å² / B_iso min: 3.43 Å²

Refinement step

Cycle: final / Resolution: 2.36→52.872 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6715	0	228	414	7357
B_iso mean	-	-	39.31	36.41	-
Num. residues	-	-	-	-	845

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6993
X-RAY DIFFRACTION	f_angle_d	1.057	9448
X-RAY DIFFRACTION	f_chiral_restr	0.049	1047
X-RAY DIFFRACTION	f_plane_restr	0.005	1180
X-RAY DIFFRACTION	f_dihedral_angle_d	15.32	4254

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.36-2.419	0.2884	132	0.2118	2558	2690	93
2.419-2.4844	0.2972	147	0.197	2676	2823	94
2.4844-2.5575	0.2571	143	0.1881	2607	2750	93
2.5575-2.6401	0.2687	136	0.1936	2593	2729	93
2.6401-2.7344	0.3049	130	0.182	2604	2734	92
2.7344-2.8439	0.2775	150	0.1835	2608	2758	92
2.8439-2.9733	0.2448	140	0.1891	2556	2696	91
2.9733-3.1301	0.2864	116	0.1851	2529	2645	89
3.1301-3.3262	0.2572	108	0.1677	2297	2405	82
3.3262-3.5829	0.2152	138	0.1489	2568	2706	93
3.5829-3.9434	0.179	143	0.1243	2715	2858	95
3.9434-4.5137	0.1609	139	0.1173	2640	2779	94
4.5137-5.6858	0.1907	138	0.1275	2568	2706	92
5.6858-52.8853	0.1639	138	0.1458	2563	2701	91

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	0.1618	-0.1727	0.3346	0.0937	0.1907	0.151	0.2565	-0.2412	-0.1334	0.0116	-0.0778	0.0161	0.5074	-0.0192	0.0033	0.3009	-0.0976	-0.02	0.3164	0.0707	0.1308	6.6582	-12.8812	18.5076
2	0.077	-0.2407	-0.2783	0.2821	-0.0658	0.319	0.0041	0.0115	-0.168	0.0034	0.0186	-0.1885	0.1534	0.0482	-0.0001	0.1746	-0.0145	0.0159	0.2464	-0.0198	0.2418	11.6793	-13.2827	-5.6656
3	0.5271	-0.1849	-0.2008	0.694	0.577	0.6739	-0.1587	-0.4418	0.169	0.0425	0.4649	-0.1067	0.1253	0.594	0.0847	0.1268	0.0552	-0.0226	0.2377	-0.0225	0.1872	14.6527	-2.4404	1.2682
4	0.2272	-0.0373	0.007	0.0216	-0.2032	0.3775	0.1988	-0.0767	-0.1205	0.197	-0.247	0.1402	0.4765	-0.0333	-0.0019	0.3469	-0.0473	-0.0344	0.3338	0.0154	0.2226	0.2976	-16.6585	7.6028
5	1.1977	-0.2626	0.1111	0.8169	0.6638	0.4561	-0.0113	-0.0259	0.2165	-0.0474	-0.1326	0.2655	-0.1763	-0.2321	-0.0179	0.1654	-0.0103	-0.013	0.1056	0.0086	0.2051	-5.4092	5.5324	-6.432
6	0.1761	-0.03	-0.0659	0.1213	0.039	0.2745	-0.0131	0.0566	0.0767	-0.1176	-0.2004	0.28	-0.0791	-0.3011	0	0.1944	0.0244	0.0024	0.2387	-0.0914	0.3848	-12.1511	10.1396	-3.2145
7	0.3723	-0.2559	0.341	0.3243	-0.0025	0.9279	-0.0472	-0.2566	0.1918	0.0172	-0.0661	0.3214	-0.1819	-0.2119	-0.0051	0.1906	-0.008	0.0897	0.2536	-0.1514	0.3006	-14.5231	8.0583	10.6349
8	0.0032	0.206	-0.0408	0.6575	-0.4523	0.3793	0.0185	-0.0149	0.0445	-0.275	0.0078	0.1686	-0.0705	0.0014	0	0.1953	0.0012	0.0035	0.1219	-0.0008	0.1736	7.3268	1.8306	-20.3103
9	0.5199	0.3682	0.3888	1.0196	-0.0982	0.326	-0.1293	-0.2176	0.105	0.2136	-0.0965	0.0647	0.1195	-0.0242	-0.0228	0.1455	-0.0202	-0.0026	0.182	-0.0538	0.1709	2.7764	7.5993	2.872
10	1.0788	0.0135	0.2095	0.1695	0.2568	0.3537	0.0499	0.0958	-0.8539	-0.1257	0.0677	0.0634	0.3279	-0.4316	0.007	0.1532	-0.0199	-0.0515	0.2008	0.06	0.1493	-7.8071	-1.837	-19.8634
11	0.0978	-0.2848	0.2766	-0.0519	-0.0578	0.2014	0.1776	0.3362	-0.1865	-0.3676	-0.1646	0.0641	0.2481	-0.1572	-0.0209	0.3646	0.0523	-0.099	0.4392	-0.0308	0.1674	-31.652	-25.4415	-52.4852
12	0.1115	0.1066	-0.0761	0.3395	0.2863	0.3993	0.112	0.0321	-0.0335	-0.1033	-0.1776	0.3109	0.0977	-0.1827	-0.0359	0.2006	0.0426	-0.082	0.2213	-0.0158	0.1663	-33.7523	-20.9494	-29.3917
13	0.5273	0.2743	0.025	0.4192	0.0743	0.7886	0.508	0.2974	0.3018	-0.1424	-0.4176	0.187	-0.5428	-0.575	0.0435	0.2367	0.1503	-0.0272	0.2902	0.0841	0.2494	-28.9974	-12.8664	-34.9594
14	0.5056	0.0087	-0.3039	0.1518	0.2038	0.4105	-0.1296	0.3192	-0.3363	-0.2516	0.0273	-0.1211	0.0669	-0.378	-0.0202	0.2422	0.0011	-0.08	0.272	-0.048	0.2146	-31.4388	-32.8394	-41.6161
15	1.104	0.0325	0.1899	0.6279	-0.1257	0.2294	-0.0365	-0.0308	-0.0149	-0.0706	-0.0268	-0.1266	0.108	0.0863	0.0001	0.1442	0.0235	0.0152	0.1433	0.0086	0.1928	-11.1263	-24.3789	-25.8784
16	0.4676	-0.1485	0.2226	0.1246	0.1346	0.4131	-0.1001	0.1074	0.0865	-0.2043	0.1145	0.0018	0.0662	0.086	0	0.1709	0.0109	0.0408	0.1692	0.0118	0.2662	-3.1819	-27.0683	-29.2546
17	0.6306	-0.2254	0.498	0.3647	-0.1125	0.606	0.0657	0.3276	-0.071	-0.1323	0.0355	-0.1574	0.0585	0.1898	-0	0.2865	-0.0109	0.0661	0.2525	-0.017	0.2313	-2.8191	-30.0109	-43.276
18	0.2161	0.3828	0.2859	0.3323	0.2223	0.3188	-0.0381	-0.1243	0.0503	0.0825	-0.0125	-0.1204	0.1002	-0.0844	0.0001	0.1605	0.002	0.0061	0.1787	0.0247	0.1801	-22.7316	-16.3807	-12.813
19	0.116	0.109	-0.0611	0.5356	0.2902	0.3301	0.137	-0.3683	0.1376	0.0322	0.003	0.0623	0.3508	-0.2094	0.0093	0.2533	0.0155	-0.0456	0.1785	0.0323	0.1809	-17.1079	-30.388	-13.5231

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 -6 through 36 )	A	-6 - 36
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 72 )	A	37 - 72
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 105 )	A	73 - 105
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 106 through 147 )	A	106 - 147
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 148 through 202 )	A	148 - 202
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 203 through 234 )	A	203 - 234
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 235 through 298 )	A	235 - 298
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 299 through 349 )	A	299 - 349
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 350 through 412 )	A	350 - 412
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 413 through 437 )	A	413 - 437
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -6 through 36 )	B	-6 - 36
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 37 through 72 )	B	37 - 72
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 73 through 105 )	B	73 - 105
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 106 through 147 )	B	106 - 147
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 148 through 202 )	B	148 - 202
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 203 through 234 )	B	203 - 234
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 235 through 298 )	B	235 - 298
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 299 through 349 )	B	299 - 349
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 413 through 436 )	B	413 - 436

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 426 molecules

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Experiment

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 6 types, 426 molecules

-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

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Movie

-
Structure viewers

+
Viewer log

-
This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 426 molecules

-
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

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi