PDB-6r7d: Crystal structure of LTC4S in complex with AZ13690257

ID or keywords:

Entry

Database: PDB / ID: 6r7d

Title

Crystal structure of LTC4S in complex with AZ13690257

Components

Leukotriene C4 synthase

Keywords

MEMBRANE PROTEIN / Inhibitor / arachidonic acid cascade / cysteinyl leukotrienes

Function / homology

Function and homology information

Biosynthesis of protectin and resolvin conjugates in tissue regeneration (PCTR and RCTR) / Biosynthesis of maresin conjugates in tissue regeneration (MCTR) / leukotriene-C4 synthase / leukotriene-C4 synthase activity / Biosynthesis of Lipoxins (LX) / Synthesis of 5-eicosatetraenoic acids / leukotriene metabolic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / Synthesis of Leukotrienes (LT) and Eoxins (EX) / glutathione peroxidase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Kack, H. / Ek, M.

Citation

Journal: J.Med.Chem. / Year: 2019
Title: Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid ...
Authors: Munck Af Rosenschold, M. / Johannesson, P. / Nikitidis, A. / Tyrchan, C. / Chang, H.F. / Ronn, R. / Chapman, D. / Ullah, V. / Nikitidis, G. / Glader, P. / Kack, H. / Bonn, B. / Wagberg, F. / ...

History

Deposition	Mar 28, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2019	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.title / _citation_author.name
Revision 1.2	Nov 13, 2019	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Jan 24, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_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.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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6r7d.cif.gz	681.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6r7d.ent.gz	557.3 KB	Display	PDB format
PDBx/mmJSON format	6r7d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6r7d_validation.pdf.gz	10.3 MB	Display	wwPDB validaton report
Full document	6r7d_full_validation.pdf.gz	10.4 MB	Display
Data in XML	6r7d_validation.xml.gz	75.4 KB	Display
Data in CIF	6r7d_validation.cif.gz	92.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r7/6r7d ftp://data.pdbj.org/pub/pdb/validation_reports/r7/6r7d	HTTPS FTP

-
Related structure data

Related structure data	3pcvS S: Starting model for refinement
Similar structure data	7cc8-d 3b29-1 5kck-d 1ghb-2 855 2x93-d 4zrp-2 5o5l-5 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

3pcvS

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Leukotriene C4 synthase

B: Leukotriene C4 synthase

C: Leukotriene C4 synthase

D: Leukotriene C4 synthase

E: Leukotriene C4 synthase

F: Leukotriene C4 synthase

G: Leukotriene C4 synthase

H: Leukotriene C4 synthase

I: Leukotriene C4 synthase

J: Leukotriene C4 synthase

K: Leukotriene C4 synthase

L: Leukotriene C4 synthase

hetero molecules

227 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Leukotriene C4 synthase

B: Leukotriene C4 synthase

C: Leukotriene C4 synthase

hetero molecules

defined by author&software
58.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Leukotriene C4 synthase

E: Leukotriene C4 synthase

F: Leukotriene C4 synthase

hetero molecules

defined by author&software
56.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Leukotriene C4 synthase

H: Leukotriene C4 synthase

I: Leukotriene C4 synthase

hetero molecules

defined by author&software
55.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: Leukotriene C4 synthase

K: Leukotriene C4 synthase

L: Leukotriene C4 synthase

hetero molecules

defined by author&software
56.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.591, 169.385, 174.478
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

-
Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJKL

#1: Protein	Leukotriene C4 synthase / LTC4 synthase / Leukotriene-C(4) synthase Mass: 17482.621 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTC4S / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16873, leukotriene-C4 synthase
#5: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM

-
Non-polymers , 4 types, 160 molecules

#2: Chemical	ChemComp-JUQ / (1~{S},2~{S})-2-[5-[cyclopropylmethyl(naphthalen-1-yl)amino]-4-methoxy-pyrimidin-2-yl]carbonylcyclopropane-1-carboxylic acid Mass: 417.457 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₄H₂₃N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#4: Chemical	... ChemComp-PLM / PALMITIC ACID Mass: 256.424 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 97 / 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: 4.28 Å³/Da / Density % sol: 71.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: CaCl2, PEG400, Hepes

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 2.35→170 Å / Num. obs: 150050 / % possible obs: 99.2 % / Redundancy: 6.4 % / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.35→2.39 Å / Num. unique obs: 7388

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0135 2015/10/01	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PCV

3pcv

Resolution: 2.35→121.534 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.916 / SU B: 10.286 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2297	7340	-	random
R_work	0.2081	-	-	-
all	0.209	-	-	-
obs	-	149953	99.957 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 57.935 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.673 Å²	-0 Å²	-0 Å²
2-	-	-0.176 Å²	0 Å²
3-	-	-	0.849 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→121.534 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14126	0	928	97	15151

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.019	15472
X-RAY DIFFRACTION	r_bond_other_d	0.016	0.02	15356
X-RAY DIFFRACTION	r_angle_refined_deg	2.244	2.008	20916
X-RAY DIFFRACTION	r_angle_other_deg	2.018	3	34886
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.412	5	1778
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.199	19.871	620
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.445	15	2126
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.811	15	152
X-RAY DIFFRACTION	r_chiral_restr	0.139	0.2	2282
X-RAY DIFFRACTION	r_gen_planes_refined	0.016	0.021	17138
X-RAY DIFFRACTION	r_gen_planes_other	0.013	0.02	3910
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	7158
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	25352
X-RAY DIFFRACTION	r_nbtor_refined	0.206	0.2	14834
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	15604
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	180
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.215	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.369	0.2	70
X-RAY DIFFRACTION	r_nbd_other	0.464	0.2	231
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.177	0.2	2
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.042	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.885	3.53	7148
X-RAY DIFFRACTION	r_mcbond_other	2.883	3.53	7147
X-RAY DIFFRACTION	r_mcangle_it	3.829	5.284	8914
X-RAY DIFFRACTION	r_mcangle_other	3.828	5.284	8915
X-RAY DIFFRACTION	r_scbond_it	4.898	4.419	8324
X-RAY DIFFRACTION	r_scbond_other	4.898	4.42	8325
X-RAY DIFFRACTION	r_scangle_it	7.062	6.326	11930
X-RAY DIFFRACTION	r_scangle_other	7.062	6.326	11931
X-RAY DIFFRACTION	r_lrange_it	8.15	30.571	17257
X-RAY DIFFRACTION	r_lrange_other	8.141	30.564	17252
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.062	0.05	17396
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.076	0.05	16862
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.041	0.05	17512
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.06	0.05	17400
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.082	0.05	16994
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.051	0.05	17600
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.066	0.05	17206
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.076	0.05	16888
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.052	0.05	17540
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.062	0.05	17268
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.082	0.05	16850
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.063	0.05	17050
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.063	0.05	17254
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.043	0.05	17586
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.068	0.05	17186
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.072	0.05	17330
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.041	0.05	17518
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.063	0.05	17068
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.073	0.05	17252
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.03	0.05	17546
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.069	0.05	17024
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.077	0.05	16890
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.06	0.05	17080
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.041	0.05	17298
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.073	0.05	16922
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.055	0.05	17094
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.005	0.05	17540
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.085	0.05	16774
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.064	0.05	17030
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.028	0.05	17496
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.062	0.05	17258
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.085	0.05	17050
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.035	0.05	17534
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.073	0.05	17274
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.077	0.05	16898
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.037	0.05	17470
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.067	0.05	17298
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.075	0.05	16884
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.067	0.05	17186
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.069	0.05	17328
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.039	0.05	17454
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.06	0.05	17102
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.066	0.05	17310
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.036	0.05	17476
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.066	0.05	17056
X-RAY DIFFRACTION	r_ncsr_local_group_46	0.079	0.05	17044
X-RAY DIFFRACTION	r_ncsr_local_group_47	0.067	0.05	17326
X-RAY DIFFRACTION	r_ncsr_local_group_48	0.041	0.05	17312
X-RAY DIFFRACTION	r_ncsr_local_group_49	0.089	0.05	16866
X-RAY DIFFRACTION	r_ncsr_local_group_50	0.076	0.05	17324
X-RAY DIFFRACTION	r_ncsr_local_group_51	0.049	0.05	17280
X-RAY DIFFRACTION	r_ncsr_local_group_52	0.073	0.05	17166
X-RAY DIFFRACTION	r_ncsr_local_group_53	0.073	0.05	16936
X-RAY DIFFRACTION	r_ncsr_local_group_54	0.041	0.05	17584
X-RAY DIFFRACTION	r_ncsr_local_group_55	0.069	0.05	17196
X-RAY DIFFRACTION	r_ncsr_local_group_56	0.072	0.05	16924
X-RAY DIFFRACTION	r_ncsr_local_group_57	0.056	0.05	17112
X-RAY DIFFRACTION	r_ncsr_local_group_58	0.071	0.05	17128
X-RAY DIFFRACTION	r_ncsr_local_group_59	0.033	0.05	17688
X-RAY DIFFRACTION	r_ncsr_local_group_60	0.062	0.05	17082
X-RAY DIFFRACTION	r_ncsr_local_group_61	0.084	0.05	16790
X-RAY DIFFRACTION	r_ncsr_local_group_62	0.065	0.05	17060
X-RAY DIFFRACTION	r_ncsr_local_group_63	0.028	0.05	17522
X-RAY DIFFRACTION	r_ncsr_local_group_64	0.068	0.05	17204
X-RAY DIFFRACTION	r_ncsr_local_group_65	0.083	0.05	16766
X-RAY DIFFRACTION	r_ncsr_local_group_66	0.071	0.05	17004

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / 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 (%)	WR_factor R_work
2.35-2.411	0.316	555	0.281	10420	10976	99.9909	0.259
2.411-2.477	0.265	585	0.248	10143	10729	99.9907	0.219
2.477-2.549	0.251	514	0.218	9892	10408	99.9808	0.187
2.549-2.627	0.215	480	0.208	9635	10115	100	0.178
2.627-2.713	0.224	479	0.196	9332	9814	99.9694	0.163
2.713-2.809	0.219	457	0.174	9068	9526	99.9895	0.147
2.809-2.915	0.194	467	0.181	8727	9194	100	0.154
2.915-3.033	0.208	481	0.182	8360	8842	99.9887	0.157
3.033-3.168	0.224	423	0.19	8063	8487	99.9882	0.168
3.168-3.323	0.226	359	0.194	7774	8135	99.9754	0.174
3.323-3.502	0.197	397	0.191	7338	7736	99.9871	0.176
3.502-3.715	0.209	326	0.199	7014	7342	99.9728	0.189
3.715-3.971	0.206	300	0.195	6593	6893	100	0.188
3.971-4.289	0.217	262	0.196	6194	6458	99.969	0.192
4.289-4.697	0.208	287	0.191	5670	5961	99.9329	0.193
4.697-5.251	0.222	270	0.194	5125	5397	99.9629	0.197
5.251-6.061	0.243	256	0.238	4570	4827	99.9793	0.234
6.061-7.419	0.247	191	0.227	3884	4077	99.9509	0.231
7.419-10.472	0.185	143	0.168	3062	3216	99.658	0.188
10.472-121.534	0.407	108	0.406	1749	1884	98.5669	0.385

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	0.5575	0.7824	-0.0967	1.8483	-0.1179	1.1109	0.0539	-0.0501	-0.0099	0.2314	-0.1461	0.1364	0.0406	-0.1017	0.0922	0.1275	-0.1068	0.1113	0.0989	-0.0872	0.306	14.0891	58.623	32.6432
2	1.2485	0.6271	0.1564	1.9201	1.0038	0.9328	0.009	-0.0092	-0.0353	0.0555	-0.037	0.0779	0.1432	0.0717	0.0281	0.1342	-0.0477	0.0367	0.0804	-0.0631	0.2414	26.1902	47.7346	26.2295
3	1.9988	0.2847	0.0215	1.3947	0.0075	0.4935	0.1149	0.1314	0.0188	-0.0982	-0.1324	0.247	0.0313	-0.0991	0.0175	0.0745	-0.0492	0.0103	0.1187	-0.0795	0.2557	16.3428	57.8012	15.4036
4	1.1406	-0.4129	-0.4606	0.9733	0.8185	1.483	0.1921	0.1251	0.0417	-0.3049	-0.1937	0.0834	-0.1012	-0.032	0.0016	0.2337	0.1052	0.0832	0.1068	-0.0362	0.1731	59.108	83.8269	-6.9582
5	1.8484	-0.37	-0.6108	0.4301	-0.2568	0.8885	0.1157	-0.0122	-0.0613	-0.1078	-0.0879	-0.051	-0.0382	0.0421	-0.0278	0.1047	0.0137	0.1136	0.0859	-0.0426	0.2097	68.1142	70.8129	0.8535
6	0.9281	0.0562	-0.8033	1.3164	-0.026	1.4813	0.1601	0.041	0.2	-0.0938	-0.0058	-0.1527	-0.1771	0.0014	-0.1543	0.1193	-0.0119	0.1353	0.069	-0.0483	0.2012	72.5163	87.3878	4.0413
7	0.7252	-0.0572	0.6673	1.5202	-0.3772	1.4309	0.042	-0.0885	-0.1807	0.0926	0.0165	-0.1269	0.1821	-0.1552	-0.0585	0.1085	0.0155	-0.076	0.0582	-0.0129	0.161	-54.0776	68.069	54.0322
8	1.4784	-0.2974	0.51	0.8156	0.3627	1.7826	-0.0135	-0.3444	0.0205	0.2141	-0.0643	0.1292	0.0321	-0.1468	0.0778	0.1146	-0.0419	-0.0125	0.1853	-0.029	0.0762	-67.0498	74.9963	63.2741
9	2.0703	-0.1563	0.7217	0.5251	-0.4061	0.8617	0.0372	-0.0778	0.1507	0.1455	-0.0574	-0.1353	0.0044	-0.026	0.0202	0.1003	0.0081	-0.1171	0.1052	-0.0467	0.1944	-53.7624	85.2087	56.99
10	0.8032	0.2268	0.1376	1.3883	-0.1813	0.9292	0.0511	0.0359	0.1707	-0.0877	0.0253	0.0255	-0.1622	-0.123	-0.0764	0.1339	0.0143	0.106	0.0424	0.0782	0.3365	-35.5702	33.473	58.5464
11	1.8689	0.6567	-0.6319	1.8292	0.2303	0.5013	0.1284	0.051	-0.0102	-0.0618	0.0473	-0.1523	-0.1587	0.0563	-0.1757	0.115	-0.0669	0.0817	0.0914	0.0222	0.2871	-23.1298	26.0535	48.9176
12	0.9506	0.0826	-0.4454	1.8835	0.4493	1.6645	0.0576	-0.2237	0.2154	0.1212	0.069	-0.1311	-0.1182	0.2568	-0.1266	0.1252	-0.0491	0.0394	0.0899	-0.0151	0.292	-21.589	26.9055	66.5939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Label asym-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	-4 - 144
2	X-RAY DIFFRACTION	2	ALL	B	-4 - 144
3	X-RAY DIFFRACTION	3	ALL	C	-4 - 143
4	X-RAY DIFFRACTION	4	ALL	D	-4 - 145
5	X-RAY DIFFRACTION	5	ALL	E	-4 - 144
6	X-RAY DIFFRACTION	6	ALL	F	-4 - 145
7	X-RAY DIFFRACTION	7	ALL	G	-4 - 144
8	X-RAY DIFFRACTION	8	ALL	H	-4 - 146
9	X-RAY DIFFRACTION	9	ALL	I	-4 - 143
10	X-RAY DIFFRACTION	10	ALL	J	-4 - 144
11	X-RAY DIFFRACTION	11	ALL	K	-4 - 145
12	X-RAY DIFFRACTION	12	ALL	L	-4 - 143

-
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

-
Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJKL

-
Non-polymers , 4 types, 160 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

-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

-Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJKL

-Non-polymers , 4 types, 160 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

-
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

-
Protein / Sugars , 2 types, 13 molecules ABCDEFGHIJKL

-
Non-polymers , 4 types, 160 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