PDB-4zbi: Mcl-1 complexed with small molecules

ID or keywords:

Entry

Database: PDB / ID: 4zbi

Title

Mcl-1 complexed with small molecules

Components

Induced myeloid leukemia cell differentiation protein Mcl-1

Keywords

apoptosis/apoptosis inhibitor / Inhibitor /

Complex / apoptosis-apoptosis inhibitor complex

Function / homology

Function and homology information

positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular homeostasis /

cell fate determination / channel activity /

mitochondrial fusion /

Bcl-2 family protein complex /

BH3 domain binding / protein transmembrane transporter activity / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.5 Å

Authors

Zhao, B.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2015
Title: Discovery of tricyclic indoles that potently inhibit mcl-1 using fragment-based methods and structure-based design.
Authors: Burke, J.P. / Bian, Z. / Shaw, S. / Zhao, B. / Goodwin, C.M. / Belmar, J. / Browning, C.F. / Vigil, D. / Friberg, A. / Camper, D.V. / Rossanese, O.W. / Lee, T. / Olejniczak, E.T. / Fesik, S.W.

History

Deposition	Apr 14, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 27, 2015	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zbi.cif.gz	740.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4zbi.ent.gz	622.2 KB	Display	PDB format
PDBx/mmJSON format	4zbi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbi ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbi	HTTPS FTP

-
Related structure data

Related structure data	4zbfC C: citing same article (ref.)
Similar structure data	4hw2-4 4hw2-5 4hw3-6 6oqn-2 6qz6-d 6udx-2 4zbf-6 4zbf-5 4zbf-9 4zbf-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) 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) 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

4zbfC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (8)

Deposited unit

A: Induced myeloid leukemia cell differentiation protein Mcl-1

B: Induced myeloid leukemia cell differentiation protein Mcl-1

C: Induced myeloid leukemia cell differentiation protein Mcl-1

D: Induced myeloid leukemia cell differentiation protein Mcl-1

E: Induced myeloid leukemia cell differentiation protein Mcl-1

F: Induced myeloid leukemia cell differentiation protein Mcl-1

G: Induced myeloid leukemia cell differentiation protein Mcl-1

H: Induced myeloid leukemia cell differentiation protein Mcl-1

I: Induced myeloid leukemia cell differentiation protein Mcl-1

J: Induced myeloid leukemia cell differentiation protein Mcl-1

K: Induced myeloid leukemia cell differentiation protein Mcl-1

L: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

1

A: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

2

B: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

3

C: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

4

D: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

5

E: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

6

F: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

7

G: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

8

H: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

9

I: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

10

J: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

11

K: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

12

L: Induced myeloid leukemia cell differentiation protein Mcl-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.256, 134.015, 135.931
Angle α, β, γ (deg.)	90.00, 99.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT Mass: 17850.281 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Chemical	ChemComp-4M6 / 1-[3-(naphthalen-1-yloxy)propyl]-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinoline-2-carboxylic acid Mass: 385.455 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂₅H₂₃NO₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.61 Å³/Da / Density % sol: 52.87 %
Crystal grow	Method: evaporation / Details: PEG3350, magnesium chloride, Bis-Tris / PH range: 6.0-8.0

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07816 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 11, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07816 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. obs: 68726 / % possible obs: 90.7 % / Redundancy: 2.7 % / R_merge(I) obs: 0.06 / R_sym value: 0.049 / Net I/σ(I): 17.3
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 2 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 82.4

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1951	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 2.5→29.966 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2395	1988	2.89 %
R_work	0.1816	-	-
obs	0.1833	68687	90.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→29.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14484	0	348	177	15009

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	15116
X-RAY DIFFRACTION	f_angle_d	1.411	20370
X-RAY DIFFRACTION	f_dihedral_angle_d	18.054	5678
X-RAY DIFFRACTION	f_chiral_restr	0.066	2208
X-RAY DIFFRACTION	f_plane_restr	0.008	2582

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 (%)
2.5-2.5617	0.3641	106	0.2661	4085	X-RAY DIFFRACTION	78
2.5617-2.631	0.3392	145	0.2596	4433	X-RAY DIFFRACTION	84
2.631-2.7083	0.324	129	0.2385	4508	X-RAY DIFFRACTION	86
2.7083-2.7957	0.303	136	0.234	4599	X-RAY DIFFRACTION	87
2.7957-2.8955	0.292	144	0.2287	4724	X-RAY DIFFRACTION	90
2.8955-3.0114	0.3062	136	0.2348	4742	X-RAY DIFFRACTION	91
3.0114-3.1483	0.2882	150	0.2281	4924	X-RAY DIFFRACTION	93
3.1483-3.3141	0.2646	143	0.2201	4929	X-RAY DIFFRACTION	93
3.3141-3.5214	0.3022	146	0.2102	4997	X-RAY DIFFRACTION	94
3.5214-3.7928	0.2445	133	0.1901	4221	X-RAY DIFFRACTION	80
3.7928-4.1736	0.21	146	0.1538	4883	X-RAY DIFFRACTION	93
4.1736-4.7754	0.1854	152	0.1403	5185	X-RAY DIFFRACTION	98
4.7754-6.0085	0.2134	158	0.1517	5189	X-RAY DIFFRACTION	98
6.0085-30	0.1652	164	0.1285	5280	X-RAY DIFFRACTION	98

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	2.3099	-2.7008	-3.0372	6.2669	3.2122	4.3346	0.019	0.337	-0.9216	-0.3452	0.2003	0.7904	0.1545	-0.297	-0.0985	0.1853	-0.0723	-0.0247	0.3535	0.0399	0.3285	-9.8519	-34.1474	-7.8496
2	2.7629	0.3468	-3.331	1.2595	1.6174	7.6089	-0.6921	-0.3941	-0.5296	-0.332	0.44	-0.9329	1.0175	0.9648	-0.2732	0.7402	0.1198	-0.0695	1.2918	-0.1861	1.2115	-15.3342	-39.4767	-13.3058
3	2.9483	0.3232	0.4121	1.7471	-0.2248	2.2832	-0.0596	0.0009	0.1823	0.0105	0.1513	0.4388	-0.2033	-0.323	-0.0111	0.2709	0.0226	0.0414	0.3984	0.0682	0.3998	-11.2459	-23.297	-0.7784
4	1.9927	-1.4737	0.2758	4.7337	-2.8459	3.9763	-0.0348	-0.0612	-0.0103	-0.2961	0.0519	-0.0956	0.0891	-0.1511	-0.0371	0.2567	-0.0285	0.0313	0.3197	0.0706	0.3109	-4.3095	-30.108	-3.1651
5	0.0176	0.0432	0.1256	0.1146	0.3241	0.8979	0.1232	-0.7538	-0.8462	0.3998	-0.0336	0.6218	0.8256	-0.6613	0.265	0.3034	-0.034	0.0961	0.5533	0.2304	0.5356	-15.5082	-40.2893	5.5963
6	3.1814	2.6083	-0.1065	3.3133	-1.7441	2.4761	-0.2059	-0.072	0.3019	-0.1151	0.0002	-0.5488	0.0376	0.6482	0.2163	0.3215	0.015	-0.0331	0.3518	-0.0175	0.2283	18.8708	-0.2127	2.4951
7	2.1861	0.3418	1.3368	1.1508	-2.5298	7.6332	-0.1178	0.6535	0.9124	-0.5747	0.0477	-0.1062	-1.7641	-0.0214	0.28	1.0506	0.0777	-0.1691	1.2248	0.1201	1.0017	26.9505	3.9076	3.4359
8	0.9753	0.2884	0.5184	2.1816	0.2926	1.7722	-0.1376	-0.0572	0.0057	-0.0826	0.041	-0.0304	0.0111	0.1788	-0.0286	0.3402	0.0081	0.0472	0.3866	0.0329	0.2746	12.014	-9.674	8.027
9	1.7115	-1.3986	0.1154	3.8454	-0.6584	2.0939	0.0681	0.0403	0.0013	-0.096	-0.1822	-0.1035	-0.0649	0.0186	-0.0081	0.3183	-0.0258	0.0077	0.358	0.005	0.2251	11.1007	-5.159	4.5433
10	0.3606	-0.4043	-0.2277	1.7515	-1.1351	1.6041	-0.409	-0.7713	0.2945	0.3691	0.1243	-0.8321	-0.0563	0.6982	-0.0544	0.5155	0.0165	-0.0126	0.4228	-0.016	0.2502	11.6946	7.675	14.4731
11	5.9828	-3.9828	-0.4986	4.2554	-0.2587	3.007	-0.2587	-0.5386	0.2694	0.4082	-0.2341	-0.6433	0.2279	0.4798	-0.0584	0.3085	-0.0074	-0.0175	0.4146	0.1592	0.2802	19.8044	-37.3363	2.3711
12	3.202	-1.1097	-3.4019	0.3784	1.1765	3.618	-0.4645	-0.2721	-0.361	0.3639	-0.923	1.0912	0.2719	-0.6356	0.4423	1.149	-0.0416	0.1537	1.208	-0.0281	1.5368	24.4076	-36.198	10.7106
13	2.9968	1.16	0.731	4.2698	-2.6957	2.5101	0.1376	-0.0345	-0.1212	0.0492	-1.198	-0.8458	-0.1671	0.9869	-0.4697	0.3862	0.0805	0.011	0.6494	0.3971	0.4936	26.0305	-47.3343	1.5683
14	4.4929	-2.1016	0.5082	3.7965	1.1961	3.5147	-0.1119	0.2808	-0.1774	-0.1843	-0.2439	-0.4436	0.6586	0.5572	0.3917	0.6156	0.4382	0.535	0.9095	0.3816	0.0862	28.8874	-41.3307	-17.8668
15	4.4569	1.0268	0.5904	1.3492	0.134	1.0795	-0.536	0.0615	0.7581	-0.1564	0.0732	0.2787	0.1479	0.1674	-0.0773	0.4438	0.1169	0.0777	0.3085	0.219	0.201	19.0827	-32.4061	-15.6067
16	0.9028	0.3396	-0.5102	2.3348	-0.2684	1.5037	-0.2088	0.4221	-0.3388	-0.4913	-0.8374	-0.2804	0.5694	0.0312	-0.1588	-0.2693	0.8622	-0.2055	-0.0223	0.6748	0.2933	22.3593	-42.5631	-9.4466
17	3.1133	0.9245	-2.2101	2.5739	-0.9873	1.5645	0.3204	0.1745	0.3262	0.3135	-0.2067	0.3488	-0.138	-0.0296	-0.03	0.2671	0.0484	-0.0157	0.39	0.1036	0.2878	15.5246	-37.9375	-4.786
18	5.3142	-1.0124	0.8028	2.6376	2.8118	3.7096	0.3242	-0.4051	-0.8171	0.425	0.0465	0.2333	0.8413	0.2027	0.3025	0.3684	0.0519	0.0594	0.5507	0.2193	0.3852	18.2501	-52.7832	3.2855
19	2.3583	-2.6953	-1.3572	8.1225	-0.24	3.9694	-0.0045	-0.1125	-0.5693	0.0774	0.1868	0.6984	-0.0152	-0.2847	-0.2914	0.1998	-0.0344	-0.038	0.2476	0.0447	0.1678	37.0963	-3.2072	-58.1109
20	2.2798	-2.3909	-3.8866	3.9088	4.591	6.8044	-0.5794	-0.3409	-0.2928	0.3628	-0.1309	0.5883	0.0102	-1.2149	0.0497	0.5439	-0.0089	0.1099	0.6124	0.1358	0.4925	31.9345	-6.7992	-51.8337
21	1.1814	-0.2556	0.0394	1.0773	-0.631	2.4973	0.1208	0.1222	0.0675	-0.1835	-0.0029	0.1166	-0.1424	-0.2108	0.0104	0.3259	0.0359	-0.0237	0.3391	0.0501	0.2263	36.7962	6.8415	-66.2751
22	2.264	-0.0926	0.9391	1.3304	0.2813	2.8858	-0.0373	0.2246	-0.0637	-0.135	0.0402	0.0937	-0.0753	-0.043	0.0145	0.3289	0.0302	0.0226	0.2602	0.069	0.2593	38.0144	3.208	-65.9733
23	2.0526	-0.6474	0.2301	2.6313	0.1657	1.6447	-0.2797	-0.6481	0.0289	0.4013	0.2999	0.0966	-0.3099	0.3598	-0.0402	0.3509	0.0085	-0.0127	0.3823	0.0485	0.2291	46.9115	5.9543	-50.6086
24	3.3538	-0.5006	-0.2502	6.8044	0.3221	1.2634	0.4303	0.0995	-0.0885	0.5526	-0.4585	-0.5012	0.0583	0.4767	-0.1215	0.2731	0.0388	0.0052	0.3876	0.135	0.1772	33.6282	-17.6712	-28.0815
25	1.8705	0.8349	-1.2733	0.3758	-0.5709	0.8701	-0.9095	0.7572	-0.2241	-2.0699	-0.7551	0.4701	-0.3586	-0.1751	0.6725	1.0905	0.1263	-0.164	0.9201	-0.0353	0.8798	41.1848	-22.7561	-26.8259
26	1.8637	-0.4765	-0.8971	0.9745	0.3653	2.2117	-0.0646	-0.0658	0.1084	0.5192	-0.0088	0.0106	-0.3405	0.2404	-0.0128	0.4479	0.0381	0.0185	0.4288	0.0943	0.2862	28.927	-5.8564	-25.7876
27	1.4419	0.126	-0.1131	2.0429	-0.1582	3.5553	0.0072	-0.0646	0.0314	0.3523	-0.0746	0.224	-0.2293	-0.0431	0.0097	0.3449	0.044	0.0448	0.3431	0.0649	0.2021	27.4606	-10.4263	-29.2722
28	4.4707	0.3536	-2.4802	0.3014	-0.1244	1.6887	-0.1233	0.3918	-0.0959	-0.3087	-0.1303	-0.3549	0.1812	0.8655	0.0809	0.3093	0.0381	0.0349	0.4244	0.0604	0.1923	39.626	-11.0576	-41.5269
29	3.6387	-2.4464	0.5876	4.4863	-3.2385	5.0307	0.1351	0.229	-0.4184	-0.1207	0.0693	0.2234	0.3603	-0.9668	-0.1837	0.2717	0.0293	0.0284	0.3727	-0.0463	0.242	-5.6909	3.4976	-16.8201
30	2.4101	-0.1756	-1.0366	0.5412	-1.2966	5.0187	-0.377	-1.2705	0.2167	0.3295	-0.0822	-0.0282	0.5879	-0.6528	0.1027	0.8081	0.0305	-0.0171	1.3663	0.0321	1.0492	-14.7034	4.6303	-15.0531
31	2.1214	-0.224	0.4195	1.1344	0.0354	1.2718	-0.1974	0.5182	-0.4585	-0.5204	-0.0117	-0.0589	-0.1484	-0.3	0.0128	0.3977	0.0246	0.0833	0.4861	-0.06	0.3707	1.7153	3.019	-27.6137
32	1.568	0.7539	0.4513	3.1464	0.7224	2.3913	-0.2373	0.606	-0.4424	-0.6116	0.2946	-0.3853	-0.2901	-0.0427	-0.0634	0.3118	-0.009	0.0593	0.4283	-0.094	0.2672	3.0302	5.2918	-26.4831
33	1.3089	1.4867	1.0935	3.7176	2.634	4.3127	0.0979	0.3657	-0.8625	0.5379	0.0095	-0.3261	0.8505	-0.1547	-0.0332	0.3319	-0.0297	0.0558	0.4027	-0.102	0.3942	0.429	-3.39	-20.3335
34	1.6341	1.5295	0.127	1.4481	-0.1904	4.9218	0.0656	-0.219	0.3514	0.1858	0.1096	-0.2647	-0.5872	-0.5814	0.0496	0.4961	0.1014	-0.0268	0.3004	0.0222	0.3072	1.8265	16.3852	-14.7279
35	4.8127	-2.9851	1.3471	6.4655	-1.7634	4.6544	0.4018	-0.9982	-0.5589	0.2465	0.0106	0.4462	-0.0486	-0.6056	-0.1781	0.3928	-0.0145	0.047	0.3213	-0.02	0.1547	34.0169	-56.5636	-34.023
36	2.0007	-0.5241	5.4995	3.2409	4.1456	8.8638	-1.146	-0.8033	0.6648	0.5182	-1.1883	-0.5712	-0.7149	0.6205	-0.2065	0.6981	0.0488	0.1815	1.2908	0.4557	0.7206	29.3841	-57.4669	-26.1365
37	2.6996	0.3208	0.7348	3.0701	1.2767	2.802	0.284	-0.1529	0.3667	-0.1913	0.0633	0.1712	-0.8201	-1.0944	0.1233	0.518	0.146	0.0991	0.4764	-0.0265	0.2913	28.4344	-48.2029	-42.9451
38	1.9936	-0.9808	0.205	0.9548	-0.5759	2.6812	-0.1831	0.087	-0.3057	-0.6053	0.0969	0.1627	-0.084	-0.2092	0.0268	0.3768	-0.0017	0.0048	0.2909	-0.0549	0.2662	33.1787	-56.6853	-48.4253
39	4.9398	3.62	1.2029	4.3784	1.122	2.2839	0.361	0.2661	-0.3365	0.4378	-0.0924	-0.1306	0.1177	0.1589	-0.0093	0.3574	-0.022	0.0094	0.2712	0.0058	0.2326	40.373	-56.8622	-40.6792
40	1.3554	-2.047	-0.9342	5.3165	0.3305	1.1518	-0.0853	-0.7088	0.8391	1.1939	0.0421	-0.4511	-0.9427	-0.245	0.0546	0.9681	-0.065	0.0656	-0.2072	-0.6853	-0.1742	39.0122	-41.2705	-32.7488
41	2.3375	2.6609	1.089	8.6135	-1.9622	2.7009	0.4496	-0.0693	0.5129	0.3277	-0.1161	0.9401	0.1284	-0.4587	-0.1857	0.2155	0.1135	0.0784	0.3386	0.0282	0.2898	5.9708	-24.8817	-39.5012
42	0.94	-1.437	-1.0344	2.2105	1.4092	4.637	-1.362	-0.4631	-1.1909	-0.5484	0.1147	0.5121	0.6079	-0.6213	-0.4619	0.5381	0.0587	0.0002	0.8227	0.1829	0.653	1.3057	-20.7677	-45.9413
43	3.3808	1.0034	-1.2436	4.0357	-3.8693	8.1178	-0.1946	0.073	-0.6073	-0.9631	-0.0867	0.0761	1.2194	-0.7926	-0.1754	0.43	-0.0669	-0.0109	0.3058	0.0516	0.4676	3.6952	-35.3786	-44.7313
44	2.937	0.2572	-0.0726	2.2187	0.0064	2.5694	-0.2063	-0.4672	-0.0729	0.338	0.2002	0.1897	0.4017	-0.2073	0.0267	0.4385	0.0607	0.1456	0.3805	0.121	0.2199	7.8313	-35.2508	-23.6664
45	2.5727	0.3857	-1.0454	2.208	0.5913	2.7902	-0.0252	-0.3015	-0.1274	0.2564	0.1141	0.1405	0.2469	-0.2045	0.0235	0.3357	0.0586	0.0357	0.3942	0.1201	0.2664	7.5121	-31.6754	-31.8033
46	3.08	0.7235	0.2005	2.1078	-0.6726	1.6101	-0.2966	0.2145	-0.3432	-0.746	0.2877	-0.0038	0.4013	0.1028	-0.0461	0.418	0.0851	0.0212	0.3161	-0.0182	0.2682	16.7459	-33.1465	-46.5618
47	3.8514	-3.0786	1.359	8.5235	-0.6742	0.7775	0.2886	0.1705	0.077	-1.0117	-0.2359	-0.538	-0.2712	0.5247	-0.0564	0.3053	0.01	0.0246	0.4539	0.0643	0.2412	2.9317	-9.3019	-69.296
48	7.8994	1.1643	2.3629	1.3592	1.7173	2.2999	-1.2663	-0.7987	1.4184	1.6535	1.2773	-0.2711	1.0356	2.0676	-0.6928	1.0663	-0.159	0.1448	0.9406	0.0208	0.9888	10.5655	-4.4649	-70.3431
49	2.4154	0.8355	0.3499	1.1867	0.4079	1.9983	0.0092	0.2433	-0.1441	-0.2698	-0.04	-0.1069	0.2862	0.3477	-0.0256	0.4518	0.0709	0.0311	0.4787	0.0644	0.3145	-1.2315	-21.2979	-71.862
50	1.3984	-0.047	0.6842	1.3078	0.2327	2.3273	0.0928	0.3557	-0.0727	-0.4196	-0.0478	-0.0438	-0.1359	-0.1965	-0.013	0.4338	0.0825	-0.0211	0.392	0.0244	0.22	-2.7792	-17.6825	-71.724
51	6.0045	1.2607	-3.2031	2.0851	0.9315	3.6785	0.0929	-0.2874	-0.2308	0.4694	0.0907	-0.0356	0.1636	0.7196	-0.0375	0.2958	-0.0133	-0.0694	0.3695	0.0563	0.2674	-4.3123	-12.9386	-53.9969
52	0.6309	0.3524	-0.171	0.3217	-0.2916	0.8628	0.1419	0.1359	0.2435	0.1669	-0.1228	-0.171	-0.1547	0.0504	0.0339	0.2939	0.049	-0.0342	0.3336	0.0335	0.3791	7.7613	-15.8875	-56.2455
53	4.6775	-0.7656	2.4579	5.6808	-3.0613	5.3381	0.0353	0.0585	0.1744	-1.0162	0.0618	-1.0143	-0.0832	0.8849	0.1286	0.2652	-0.1326	0.0212	0.5039	0.0065	0.2391	0.6418	-64.7817	-41.7677
54	3.7716	0.4403	2.7903	0.0518	0.3253	2.0584	-1.4026	-1.2293	0.8719	1.4285	0.62	-0.3064	-1.2601	-0.4388	-0.5269	1.176	-0.103	0.4299	1.0436	-0.1698	1.2514	8.4748	-61.8666	-46.319
55	2.9111	-0.0771	0.1088	1.1937	1.7921	2.7067	0.0107	0.125	-0.2323	-0.1707	0.3826	-1.1311	-0.0703	0.8527	0.1711	0.2511	-0.0957	0.0314	1.0618	0.063	0.417	8.905	-68.0325	-33.6644
56	5.3043	0.2177	5.197	1.8387	0.4826	9.2748	-0.1267	-0.2614	-0.8882	-0.0529	-0.2242	-0.6425	0.998	-0.2201	-0.2594	0.4067	0.0108	0.0354	0.4678	0.0713	0.366	-4.0833	-85.1507	-35.5096
57	1.519	0.7613	0.1874	1.6643	0.362	0.3177	-0.0173	0.0877	-0.1439	-0.1094	-0.0105	-0.05	0.115	0.3288	0.0079	0.2778	-0.0195	-0.0526	0.476	0.0125	0.1804	-6.004	-75.2321	-35.0883
58	0.21	0.7379	0.5461	3.2869	0.9931	3.4867	-0.1247	0.3668	-0.3478	-1.1176	-0.094	0.1978	-0.3481	0.0376	0.0074	0.3906	-0.0167	0.0098	0.5227	-0.0298	0.3099	-5.9934	-71.8771	-42.9051
59	2.4026	-0.7819	1.9805	2.9378	1.0838	2.7283	0.2091	0.0503	0.06	0.7105	0.135	-0.5392	-0.1398	0.4387	0.093	0.1636	-0.4297	-0.1768	0.272	-0.1239	0.1631	-6.0889	-58.299	-27.2486
60	0.2274	-0.5481	-0.4967	1.3658	1.2382	1.2006	-0.1368	0.2072	0.4132	0.361	-0.0904	-1.1397	-0.6927	0.4991	0.4903	0.0714	-0.2741	-0.3916	0.7769	0.0966	0.2687	6.7603	-60.43	-27.6646
61	3.2629	-1.4822	-1.6864	4.3585	-3.1481	6.0585	-0.3524	-0.4037	-0.6453	-0.0816	-0.2944	-0.9116	0.678	1.1419	0.3179	0.492	0.1254	0.0913	0.3887	0.0599	0.4174	32.764	-28.5418	35.093
62	1.9408	-1.1522	1.6192	0.9514	-0.5825	3.0875	-0.1405	-0.3449	-0.1432	0.4931	-0.5421	0.1199	0.6323	-0.4313	0.5614	1.0437	0.269	0.0207	1.4226	0.2329	1.2751	40.5713	-32.4961	35.9383
63	2.0821	-1.3889	-0.9798	7.3303	0.3514	0.8115	-0.3206	0.461	-0.431	-0.3599	-0.2402	-0.2051	0.467	0.0751	0.1288	0.5174	0.072	0.0983	0.5509	0.018	0.3886	30.7472	-23.4503	22.7547
64	2.0821	-0.1205	-0.84	2.3396	-0.6776	2.4529	-0.1695	-0.1052	0.0626	0.0409	-0.0419	0.0504	0.4004	0.0378	0.0052	0.4136	-0.001	-0.0001	0.3934	0.011	0.2524	24.4765	-20.9567	31.9676
65	5.3945	2.3263	3.4161	4.6155	-2.2876	7.0913	-0.4105	0.1437	-1.1881	-0.8944	0.031	-0.1565	0.6108	0.3348	0.076	1.2005	0.0511	0.357	0.3901	0.0069	0.6279	27.4932	-38.2405	24.637
66	1.471	0.6296	1.4135	4.2	-4.0124	7.8734	-0.2041	0.0678	-0.111	-0.234	0.0921	0.6996	0.1895	-0.8794	-0.1328	0.4795	-0.0283	-0.0551	0.2553	0.0203	0.3627	28.044	-32.7675	-83.0403
67	4.5968	-2.2155	-3.7335	2.5399	0.9295	3.5172	-0.777	1.1283	-1.1475	-0.609	0.1247	-0.2037	2.3586	-0.1297	0.4493	0.9474	0.0714	-0.094	1.2117	-0.0713	1.103	19.2819	-34.198	-84.9777
68	1.8048	0.0667	-1.6946	4.3748	2.9419	4.6294	0.1576	-0.074	-0.105	0.5105	-0.2288	0.613	0.1175	-0.9201	0.0403	0.6212	-0.0749	0.1233	0.4158	-0.0044	0.3591	26.3766	-41.7218	-75.1648
69	1.9033	0.0418	-0.8249	2.0671	-0.66	2.1282	0.1147	-0.5146	0.3028	0.1607	0.1268	0.1617	0.106	-0.2859	-0.0181	0.6121	0.0121	-0.043	0.4032	-0.019	0.3066	39.0595	-25.2555	-69.0511
70	2.2768	0.9506	-0.7942	2.7502	0.236	2.8473	-0.0574	0.0401	-0.0417	-0.1131	-0.0952	-0.0551	0.0023	-0.1359	0.0396	0.5071	0.0026	0.0294	0.2657	0.046	0.311	35.9455	-32.4564	-77.3402
71	3.2325	-0.8237	-0.0516	4.0671	-0.3836	5.3982	-0.3186	0.3376	-0.345	-0.2101	-0.0527	0.4579	0.6505	-0.4701	-0.0223	0.8801	0.0442	0.2281	0.0401	-0.1817	0.4508	31.6039	-47.6427	-80.8905

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 171 through 191 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 192 through 202 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 203 through 280 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 281 through 310 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 311 through 322 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 171 through 191 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 192 through 202 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 203 through 255 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 256 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 311 through 323 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 171 through 191 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 192 through 202 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 203 through 223 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 224 through 235 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 236 through 254 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 255 through 280 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 281 through 310 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 311 through 321 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 171 through 191 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 192 through 202 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 203 through 255 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 256 through 301 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 302 through 322 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 171 through 191 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 192 through 202 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 203 through 254 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 255 through 310 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 311 through 322 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 171 through 191 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 192 through 202 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 203 through 254 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 255 through 280 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 281 through 301 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 302 through 321 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 171 through 191 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 192 through 202 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 203 through 235 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 236 through 283 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 284 through 308 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 309 through 322 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 171 through 191 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 192 through 202 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 203 through 223 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 224 through 254 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 255 through 301 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 302 through 321 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 171 through 191 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 192 through 202 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 203 through 254 )
50	X-RAY DIFFRACTION	50	chain 'I' and (resid 255 through 301 )
51	X-RAY DIFFRACTION	51	chain 'I' and (resid 302 through 310 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 311 through 321 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 171 through 191 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 192 through 202 )
55	X-RAY DIFFRACTION	55	chain 'J' and (resid 203 through 223 )
56	X-RAY DIFFRACTION	56	chain 'J' and (resid 224 through 239 )
57	X-RAY DIFFRACTION	57	chain 'J' and (resid 240 through 280 )
58	X-RAY DIFFRACTION	58	chain 'J' and (resid 281 through 301 )
59	X-RAY DIFFRACTION	59	chain 'J' and (resid 302 through 310 )
60	X-RAY DIFFRACTION	60	chain 'J' and (resid 311 through 322 )
61	X-RAY DIFFRACTION	61	chain 'K' and (resid 171 through 191 )
62	X-RAY DIFFRACTION	62	chain 'K' and (resid 192 through 202 )
63	X-RAY DIFFRACTION	63	chain 'K' and (resid 203 through 235 )
64	X-RAY DIFFRACTION	64	chain 'K' and (resid 236 through 310 )
65	X-RAY DIFFRACTION	65	chain 'K' and (resid 311 through 320 )
66	X-RAY DIFFRACTION	66	chain 'L' and (resid 171 through 191 )
67	X-RAY DIFFRACTION	67	chain 'L' and (resid 192 through 202 )
68	X-RAY DIFFRACTION	68	chain 'L' and (resid 203 through 223 )
69	X-RAY DIFFRACTION	69	chain 'L' and (resid 224 through 254 )
70	X-RAY DIFFRACTION	70	chain 'L' and (resid 255 through 310 )
71	X-RAY DIFFRACTION	71	chain 'L' and (resid 311 through 321 )

-
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