PDB-5ggs: PD-1 in complex with pembrolizumab Fab

ID or keywords:

Entry

Database: PDB / ID: 5ggs

Title

PD-1 in complex with pembrolizumab Fab

Components

Programmed cell death protein 1
heavy chain
light chain

Keywords

IMMUNE SYSTEM /

antibody

Function / homology

Function and homology information

negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process /

humoral immune response / PD-1 signaling /

regulation of immune response / Potential therapeutics for SARS ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.997 Å

Authors

Heo, Y.S.

Citation

Journal: Nat Commun / Year: 2016
Title: Structural basis of checkpoint blockade by monoclonal antibodies in cancer immunotherapy
Authors: Lee, J.Y. / Lee, H.T. / Shin, W. / Chae, J. / Choi, J. / Kim, S.H. / Lim, H. / Won Heo, T. / Park, K.Y. / Lee, Y.J. / Ryu, S.E. / Son, J.Y. / Lee, J.U. / Heo, Y.S.

History

Deposition	Jun 16, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ggs.cif.gz	445.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ggs.ent.gz	379.7 KB	Display	PDB format
PDBx/mmJSON format	5ggs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gg/5ggs ftp://data.pdbj.org/pub/pdb/validation_reports/gg/5ggs	HTTPS FTP

-
Related structure data

Related structure data	5ggqC 5ggrC 5ggtC 5gguC 5ggvC C: citing same article (ref.)
Similar structure data	5tz2-d 6nmu-1 5ggv-d 6otc-2 4tsb-d 6svl-4 1nbz-d 5x8l-1 4wv1-2 6nmr-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#204 - Dec 2016 PD-1 similarity (3) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #247 - Jul 2020 Myelin-associated Glycoprotein similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #62 - Feb 2005 Major Histocompatibility Complex similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#204 - Dec 2016
PD-1
similarity (3)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#247 - Jul 2020
Myelin-associated Glycoprotein
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (1)

Deposited unit

A: heavy chain

B: light chain

C: heavy chain

D: light chain

Y: Programmed cell death protein 1

Z: Programmed cell death protein 1

126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: heavy chain

B: light chain

Z: Programmed cell death protein 1

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

2

C: heavy chain

D: light chain

Y: Programmed cell death protein 1

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

Unit cell

Length a, b, c (Å)	54.170, 54.195, 104.039
Angle α, β, γ (deg.)	105.69, 96.99, 96.06
Int Tables number	1
Space group name H-M	P1

#1: Antibody	heavy chain Mass: 25237.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Antibody	light chain / Mass: 23768.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein	Programmed cell death protein 1 / / hPD-1 Mass: 13883.409 Da / Num. of mol.: 2 / Fragment: UNP residues 26-148 / Mutation: C93S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: Q15116
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM MES, pH 6.5, 12% PEG500 MME, 6% PEG20,000, 50 mM ammonium acetate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.99→50 Å / Num. obs: 71844 / % possible obs: 95.2 % / Redundancy: 1.9 % / Net I/σ(I): 20.1

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 1.997→30.038 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.228	3604	5.02 %
R_work	0.1795	-	-
obs	0.1819	71844	94.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.997→30.038 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8443	0	0	796	9239

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8653
X-RAY DIFFRACTION	f_angle_d	1.165	11752
X-RAY DIFFRACTION	f_dihedral_angle_d	13.046	3121
X-RAY DIFFRACTION	f_chiral_restr	0.049	1310
X-RAY DIFFRACTION	f_plane_restr	0.005	1517

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 (%)
1.9975-2.0237	0.2675	114	0.2163	2341	X-RAY DIFFRACTION	84
2.0237-2.0515	0.2693	154	0.2213	2595	X-RAY DIFFRACTION	95
2.0515-2.0808	0.2818	125	0.2245	2604	X-RAY DIFFRACTION	91
2.0808-2.1118	0.3009	142	0.2224	2594	X-RAY DIFFRACTION	96
2.1118-2.1448	0.2637	161	0.2091	2642	X-RAY DIFFRACTION	96
2.1448-2.18	0.2466	143	0.1994	2704	X-RAY DIFFRACTION	96
2.18-2.2175	0.2532	125	0.1959	2612	X-RAY DIFFRACTION	96
2.2175-2.2578	0.295	133	0.2107	2587	X-RAY DIFFRACTION	91
2.2578-2.3013	0.2846	116	0.2025	2609	X-RAY DIFFRACTION	95
2.3013-2.3482	0.2604	143	0.1888	2691	X-RAY DIFFRACTION	96
2.3482-2.3992	0.2691	126	0.1997	2655	X-RAY DIFFRACTION	97
2.3992-2.455	0.2583	140	0.2002	2697	X-RAY DIFFRACTION	96
2.455-2.5164	0.2805	153	0.1965	2666	X-RAY DIFFRACTION	97
2.5164-2.5844	0.2721	139	0.1951	2702	X-RAY DIFFRACTION	96
2.5844-2.6604	0.2701	128	0.1943	2644	X-RAY DIFFRACTION	97
2.6604-2.7462	0.2478	142	0.1889	2624	X-RAY DIFFRACTION	95
2.7462-2.8443	0.2529	163	0.1834	2667	X-RAY DIFFRACTION	96
2.8443-2.9581	0.2418	141	0.1831	2588	X-RAY DIFFRACTION	95
2.9581-3.0926	0.2533	155	0.1784	2659	X-RAY DIFFRACTION	95
3.0926-3.2554	0.2072	138	0.1726	2644	X-RAY DIFFRACTION	96
3.2554-3.4591	0.2219	129	0.1671	2617	X-RAY DIFFRACTION	94
3.4591-3.7258	0.1941	150	0.1547	2537	X-RAY DIFFRACTION	92
3.7258-4.0999	0.1806	140	0.1512	2567	X-RAY DIFFRACTION	93
4.0999-4.6912	0.166	107	0.1381	2675	X-RAY DIFFRACTION	95
4.6912-5.903	0.1787	144	0.1637	2688	X-RAY DIFFRACTION	97
5.903-30.0415	0.2198	153	0.2039	2631	X-RAY DIFFRACTION	96

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	3.265	-1.42	-0.3535	2.9436	0.7726	1.5132	0.0659	0.5674	0.1138	-0.4511	-0.0794	0.2048	-0.0814	-0.0719	0.048	0.2366	-0.0363	0.0029	0.2286	-0.0011	0.1726	0.5312	-11.8737	-16.9038
2	3.3817	0.2414	0.3637	2.3377	0.0155	-0.0296	0.0321	-0.1204	-0.1646	0.142	-0.0558	0.1232	0.2352	0.0181	-0.0245	0.2477	-0.0146	0.0096	0.1782	0.0037	0.1588	0.0886	-18.182	-10.945
3	2.0844	-1.8924	-1.483	1.7757	1.2652	1.839	-0.0495	-0.0099	0.0126	-0.0556	0.069	0.0154	-0.0317	0.0554	-0.0059	0.1531	-0.0368	-0.0015	0.1139	0.0007	0.1642	-4.7842	1.0409	-4.1245
4	2.3932	0.5091	-0.4958	4.1911	-0.3053	2.177	0.0175	0.1938	-0.0938	0.1829	-0.0123	-0.2831	-0.1953	0.0406	-0.0143	0.123	-0.0084	-0.0116	0.1911	0.0074	0.1436	-12.2696	12.8212	0.862
5	2.6084	1.6423	1.5767	5.1349	5.8946	7.5398	-0.1952	0.1391	0.3411	-0.5942	-0.1556	0.8386	-0.4001	-0.2503	0.3015	0.2343	0.0004	-0.0444	0.2931	0.0349	0.2124	-20.3639	16.0976	-3.1867
6	2.3866	-2.5688	0.345	2.7458	-0.3688	2.8256	-0.1779	-0.1941	0.1535	0.5271	0.3029	0.2854	0.0169	0.0329	-0.0641	0.1151	0.0003	-0.0144	0.1992	-0.0018	0.1032	16.8072	0.6364	3.5696
7	3.0291	-0.6672	-0.7325	5.7959	-1.1425	2.8834	-0.0686	0.1668	-0.3879	0.2132	-0.0996	-0.6526	0.5105	0.3863	0.1103	0.2166	0.0651	0.0122	0.2193	0.0178	0.2831	23.3255	-12.0018	-1.1864
8	3.2943	0.8063	-0.5339	4.274	0.2318	2.4475	-0.0418	0.1816	0.0459	-0.2476	-0.0546	-0.1278	-0.0559	0.1095	0.062	0.1344	-0.0214	-0.0015	0.1581	-0.0133	0.1275	19.1246	-2.2906	-7.8564
9	2.6095	0.6686	-0.6945	5.4251	1.082	1.5756	0.0303	0.2824	0.2126	-0.3315	-0.0406	0.1687	-0.1326	0.0599	0.0052	0.1638	-0.002	-0.0146	0.2046	0.0333	0.1595	15.3518	3.4527	-4.4916
10	0.564	-1.0968	-1.0728	6.1546	3.1332	2.2756	-0.0213	-0.0693	0.0279	0.016	0.1367	-0.3126	0.091	0.0784	-0.1409	0.1666	0.0214	-0.0602	0.165	0.0045	0.2084	11.7253	0.0306	2.2443
11	7.8154	6.1024	2.1798	7.6126	1.5802	4.6891	-0.1462	-0.02	0.3814	-0.2249	0.0849	0.5756	0.136	-0.6768	0.0963	0.2157	0.0173	0.0095	0.2658	0.0161	0.2047	-20.0903	13.4158	12.6346
12	3.9521	2.3975	-3.7981	1.8715	-2.0591	3.5679	-0.0863	-0.2535	-0.0815	-0.0302	-0.0154	-0.0207	0.0894	0.1462	0.0705	0.1891	0.0048	-0.0163	0.1795	-0.032	0.1548	-5.0956	11.0058	14.6951
13	5.0039	1.1306	-2.8139	1.466	0.4325	3.1901	-0.2902	0.3064	-0.2425	-0.1668	0.2057	-0.0739	0.4009	-0.1238	0.115	0.154	0.0592	-0.0635	0.147	0.004	0.1517	-3.6427	9.573	10.9511
14	7.6438	1.6734	-1.5067	3.3893	0.2413	3.7494	-0.0765	-0.3052	-0.1961	0.1362	-0.1455	0.2147	0.1756	-0.3152	0.2656	0.2154	0.001	-0.0055	0.1903	0.0511	0.1397	-16.4554	8.367	20.1315
15	3.8324	2.3232	-3.7216	2.3033	-1.4199	4.2098	0.1238	-0.0615	0.7168	-0.09	-0.0511	0.1669	-0.1802	0.0094	-0.1096	0.2037	-0.0066	-0.0354	0.1171	-0.0197	0.1452	-7.7559	16.963	21.8145
16	2.571	-2.5345	-2.2129	4.841	2.036	4.1999	-0.0765	-0.3007	-0.393	0.1844	0.0833	-0.2353	0.2064	0.0207	-0.0955	0.1825	0.0277	-0.0138	0.1508	0.0506	0.1921	-9.6914	-5.7308	51.6006
17	3.3807	-0.5238	-0.9085	2.8766	0.6172	1.4439	-0.0278	-0.2521	0.0207	0.1839	0.0682	-0.0914	0.0921	0.0112	-0.0957	0.1602	-0.0165	-0.0018	0.1714	-0.0056	0.1424	-14.8889	4.4541	51.7844
18	6.2264	-0.4063	-1.4227	4.9543	0.8171	6.2561	-0.09	0.1755	-0.2201	-0.1299	-0.2972	0.5619	0.0058	-0.5044	0.1331	0.1638	-0.0211	-0.0167	0.2288	0.0311	0.2331	-24.8059	4.0828	48.7416
19	5.4568	2.2105	4.1872	4.3632	3.0553	3.7899	0.0357	-0.3293	-0.318	0.2381	-0.1045	0.1794	0.0808	-0.3279	0.0392	0.18	0.0043	0.0155	0.2085	0.0485	0.1972	-20.4618	-2.4905	54.3943
20	2.0195	-1.6505	-1.0976	1.8518	1.1386	1.6721	0.026	0.0455	-0.0373	0.0524	-0.0657	-0.0438	0.0036	-0.1057	0.055	0.1664	-0.0546	0.0024	0.1358	0.0174	0.1468	-4.679	-2.3792	42.6261
21	5.0014	1.0462	-1.1003	1.9575	1.1358	1.0816	0.1776	-0.0239	-0.2407	0.2706	-0.1103	-0.0416	-0.0461	0.0065	-0.0699	0.2425	0.0325	-0.0085	0.1508	0.0476	0.2398	11.3075	-12.3611	37.539
22	3.0384	1.0586	-0.0181	3.1852	0.5807	2.7009	-0.1482	0.5212	0.5346	0.0088	0.1617	-0.1125	-0.0097	0.3828	0.0151	0.1865	0.0031	-0.0114	0.1579	0.0285	0.1929	13.9751	-8.6904	33.8683
23	7.5977	2.6139	-4.3834	4.5804	-1.1627	6.1812	0.0095	-0.5234	-0.6638	0.4019	-0.2409	-0.4249	0.2676	0.2608	0.2467	0.2578	0.0115	-0.0758	0.2091	0.0214	0.2114	15.8578	-17.3429	40.5923
24	5.91	-2.3345	1.1555	1.1403	0.1024	1.792	0.0444	0.3345	-0.1678	-0.1137	-0.0171	-0.1401	0.0272	0.0429	-0.0295	0.2116	0.0323	0.0149	0.1332	0.037	0.1181	-2.6644	18.2093	33.5915
25	8.3788	0.8282	2.6219	3.8057	1.1495	3.3781	-0.0704	0.1319	-0.0552	0.0764	-0.0498	0.3872	-0.1123	-0.4816	0.1452	0.1679	0.0204	-0.004	0.0901	0.0573	0.1714	-15.8045	23.1138	38.4068
26	0.8796	-0.5673	-0.578	0.9913	0.4753	0.7095	0.0421	0.0144	0.0396	0.0408	-0.0039	0.0083	0.0152	-0.0496	-0.0424	0.1744	-0.0013	-0.0275	0.1738	0.0165	0.1699	-0.9981	12.1599	38.9462
27	1.1265	1.155	1.1942	3.3835	3.3714	3.445	0.011	-0.0287	0.0708	-0.0666	-0.1747	0.261	-0.0256	-0.099	0.1406	0.1413	-0.0304	0.0359	0.1725	0.0059	0.158	9.935	-2.4887	22.4063
28	1.0939	0.7118	-0.5408	6.0501	3.8415	4.541	0.1603	-0.1102	-0.0472	0.3654	-0.2191	0.1063	0.2003	-0.2704	0.061	0.1372	0.0361	-0.0151	0.1536	0.0398	0.17	8.3829	-1.1922	26.0221
29	2.4412	0.1011	-1.1254	7.5669	2.4131	3.7828	-0.0558	0.1737	-0.1215	-0.0908	-0.2959	0.3114	0.355	-0.1774	0.3097	0.2142	-0.0079	-0.0623	0.2162	0.0047	0.1536	8.5043	-14.0278	16.9459
30	1.4117	1.6589	0.5277	2.9037	2.2934	2.509	0.1108	-0.0026	-0.1013	-0.0308	-0.0927	-0.8089	-0.0837	0.1125	-0.0002	0.1412	0.005	0.0095	0.2413	0.0099	0.1681	16.1324	-4.5534	15.2365
31	6.2169	0.2784	0.8225	5.8616	0.2733	8.1995	0.047	0.4412	0.4252	0.7598	-0.0261	-0.1925	-0.866	0.2577	-0.0696	0.5177	0.0212	0.0222	0.2138	0.0731	0.4577	-28.6777	32.2056	64.8318
32	4.207	-0.4072	-0.5334	3.6539	0.87	5.6643	0.1251	0.4526	-0.1972	0.2229	-0.0146	0.7738	-0.7168	-0.7401	-0.2138	0.3593	0.1365	0.1055	0.3601	0.0121	0.5661	-39.3279	26.2983	61.8588
33	5.2295	0.4294	-1.2252	6.6879	-0.5567	5.1577	0.2934	-0.133	0.4746	-0.1185	-0.0659	0.0849	-0.9021	0.1245	-0.2579	0.3057	0.0654	0.0402	0.286	-0.059	0.3087	-24.9594	26.1023	58.8393
34	5.1027	4.8665	-2.4258	5.9787	-4.7593	5.6184	0.1455	-1.3432	-0.5249	1.3949	-0.3126	-0.6285	0.2157	0.6088	0.1668	0.8841	0.21	0.0199	0.5603	0.2472	0.7332	-27.139	13.0515	71.3459
35	3.4964	1.2683	-1.4994	5.793	0.543	1.4993	0.2182	0.1715	-0.0085	-0.5399	-0.0224	0.7127	0.0217	-0.4906	-0.0819	0.3337	0.0449	-0.0173	0.3306	0.0163	0.3006	-30.2902	18.5198	53.6005
36	2.5817	-1.352	0.1317	1.3364	-0.1031	3.4776	0.2986	0.2646	0.1759	0.2047	0.0167	0.4075	-0.2562	-0.5091	-0.2943	0.2737	0.0598	0.0846	0.3095	-0.0127	0.4474	-35.4443	23.8871	59.5767
37	3.5185	0.3426	0.5845	3.7212	1.6001	5.1303	0.3212	-1.1555	-0.4025	0.7483	-0.4305	-0.1993	0.0664	0.2555	-0.0712	0.5542	0.0962	0.0204	0.2439	0.074	0.3653	-28.9162	23.9125	65.6943
38	3.9992	-0.3891	-0.8757	6.1324	1.4973	5.8942	0.2846	-0.1664	-0.6701	0.0238	-0.3272	-0.8737	0.4051	0.7659	0.0157	0.365	0.1464	0.047	0.4499	0.0247	0.4038	31.2376	-28.3662	-24.4845
39	5.0951	-0.8235	-3.4111	9.0471	-0.9741	7.9026	0.0809	0.7443	-0.8591	-0.593	0.4499	0.1287	0.044	-0.1974	-0.4904	0.1973	0.0272	0.0195	0.2408	-0.0255	0.2876	23.9095	-23.565	-23.7774
40	4.9128	-0.8185	3.9776	5.3865	-1.3798	8.351	0.323	0.4436	-0.2107	-0.6536	-0.3074	0.2145	0.3966	-0.5571	0.1095	0.2581	0.0695	0.0293	0.4363	-0.053	0.212	18.0965	-24.2332	-26.3691
41	6.6948	1.171	0.5389	2.2936	0.6616	0.6408	0.1339	-0.7744	-1.2118	0.5286	-0.0561	-0.3933	0.2751	-0.1581	-0.0582	0.4125	0.0167	-0.024	0.4182	0.0929	0.4207	20.0115	-27.9135	-14.7603
42	4.1539	0.3298	0.9118	6.8138	0.8244	6.3014	-0.1381	0.4946	-1.0019	0.1688	0.1573	0.1795	0.9146	0.1213	0.193	0.484	0.12	0.0346	0.3282	-0.0213	0.4451	26.4498	-33.9775	-21.1393
43	2.0512	-2.4871	-1.7092	5.2879	1.9657	3.455	0.3726	0.1775	0.6628	-0.4768	-0.3859	-0.0493	-0.3497	-0.0867	-0.1319	0.4456	0.1358	0.0482	0.4812	-0.0256	0.3405	25.6606	-17.7367	-24.384
44	5.0303	0.7106	-0.5082	7.4252	-1.07	4.9396	0.1035	1.1319	-0.2814	-1.1753	-0.07	0.3036	0.5028	-0.366	0.0505	0.3733	0.0331	0.0162	0.5133	-0.0596	0.2355	26.5176	-26.8574	-31.7602

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 152 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 153 through 197 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 198 through 220 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 18 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 19 through 36 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 37 through 79 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 80 through 94 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 95 through 117 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 118 through 132 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 133 through 154 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 155 through 178 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 179 through 201 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 202 through 217 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 17 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 18 through 52 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 53 through 64 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 65 through 83 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 84 through 141 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 142 through 164 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 165 through 198 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 199 through 220 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 1 through 18 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 19 through 36 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 37 through 132 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 133 through 154 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 155 through 178 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 179 through 201 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 202 through 217 )
31	X-RAY DIFFRACTION	31	chain 'Y' and (resid 33 through 38 )
32	X-RAY DIFFRACTION	32	chain 'Y' and (resid 39 through 58 )
33	X-RAY DIFFRACTION	33	chain 'Y' and (resid 59 through 70 )
34	X-RAY DIFFRACTION	34	chain 'Y' and (resid 71 through 75 )
35	X-RAY DIFFRACTION	35	chain 'Y' and (resid 76 through 99 )
36	X-RAY DIFFRACTION	36	chain 'Y' and (resid 100 through 127 )
37	X-RAY DIFFRACTION	37	chain 'Y' and (resid 128 through 146 )
38	X-RAY DIFFRACTION	38	chain 'Z' and (resid 31 through 62 )
39	X-RAY DIFFRACTION	39	chain 'Z' and (resid 63 through 70 )
40	X-RAY DIFFRACTION	40	chain 'Z' and (resid 71 through 82 )
41	X-RAY DIFFRACTION	41	chain 'Z' and (resid 83 through 99 )
42	X-RAY DIFFRACTION	42	chain 'Z' and (resid 100 through 118 )
43	X-RAY DIFFRACTION	43	chain 'Z' and (resid 119 through 133 )
44	X-RAY DIFFRACTION	44	chain 'Z' and (resid 134 through 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

-
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