PDB-5abf: Structure of GH84 with ligand

ID or keywords:

Entry

Database: PDB / ID: 5abf

Title

Structure of GH84 with ligand

Components

(O-GLCNACASE BT_4395) x 2

Keywords

HYDROLASE /

TIM-BARREL /

INHIBITOR

Function / homology

Function and homology information

protein O-GlcNAcase /

: /

: / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / protein deglycosylation /

beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / identical protein binding
Similarity search - Function

Biological species

BACTEROIDES THETAIOTAOMICRON (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / OTHER / Resolution: 2.1 Å

Authors

Bergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Varghese, V. / Zandberg, W.F. / Shan, X. / Roth, C. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R.

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors.
Authors: Bergeron-Brlek, M. / Goodwin-Tindall, J. / Cekic, N. / Roth, C. / Zandberg, W.F. / Shan, X. / Varghese, V. / Chan, S. / Davies, G.J. / Vocadlo, D.J. / Britton, R.

History

Deposition	Aug 5, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 18, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 25, 2015	Group: Structure summary
Revision 1.2	Jan 27, 2016	Group: Database references
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5abf.cif.gz	782.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5abf.ent.gz	665.8 KB	Display	PDB format
PDBx/mmJSON format	5abf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	5abeC 5abgC 5abhC C: citing same article (ref.)
Similar structure data	5abe-1 5abh-1 5abg-2 5fl0-1 2chn-1 2xm1-1 2cho-2 5abg-1 5fl1-2 5mi4-d 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	#141 - Sep 2011 O-GlcNAc Transferase similarity (8)

Deposited unit

A: O-GLCNACASE BT_4395

B: O-GLCNACASE BT_4395

hetero molecules

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

1

A: O-GLCNACASE BT_4395

hetero molecules

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

2

B: O-GLCNACASE BT_4395

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.591, 160.989, 223.951
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

-
Protein , 2 types, 2 molecules AB

#1: Protein	O-GLCNACASE BT_4395 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE Mass: 83507.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q89ZI2, protein O-GlcNAcase
#2: Protein	O-GLCNACASE BT_4395 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B / N-ACETYL-BETA-GLUCOSAMINIDA GLUCOSAMINIDASE / GLYCOSIDE HYDROLASE Mass: 83521.422 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-737 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q89ZI2, protein O-GlcNAcase

#1: Protein

O-GLCNACASE BT_4395 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...

Mass: 83507.398 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q89ZI2,

protein O-GlcNAcase

#2: Protein

O-GLCNACASE BT_4395 / BETA-N-ACETYLGLUCOSAMINIDASE / BETA-N-ACETYLHEXOSAMINIDASE / BETA-HEXOSAMINIDASE / HEXOSAMINIDASE B ...

Mass: 83521.422 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 22-737
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q89ZI2,

protein O-GlcNAcase

-
Non-polymers , 4 types, 323 molecules

#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-XRJ / 2-[(2S,3R,4R,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)-1-pentyl-pyrrolidin-2-yl]-N-methyl-ethanamide Mass: 274.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₂₆N₂O₄
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.75 Å³/Da / Density % sol: 55.3 % / Description: NONE

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.00392
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00392 Å / Relative weight: 1
Reflection	Resolution: 2.1→80.49 Å / Num. obs: 110156 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / B_iso Wilson estimate: 39.22 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure: OTHER
Starting model: NONE

Resolution: 2.1→54.735 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 31.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2344	10409	5 %
R_work	0.206	-	-
obs	0.2074	109935	99.77 %

Solvent computation

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

Displacement parameters

B_iso mean: 66.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→54.735 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10660	0	47	318	11025

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11037
X-RAY DIFFRACTION	f_angle_d	0.784	14949
X-RAY DIFFRACTION	f_dihedral_angle_d	13.955	4180
X-RAY DIFFRACTION	f_chiral_restr	0.033	1594
X-RAY DIFFRACTION	f_plane_restr	0.004	1932

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 (%)
2.1-2.1239	0.3919	313	0.4174	6754	X-RAY DIFFRACTION	100
2.1239-2.1489	0.4225	331	0.4054	6742	X-RAY DIFFRACTION	100
2.1489-2.1751	0.4128	321	0.3803	6581	X-RAY DIFFRACTION	100
2.1751-2.2026	0.3237	322	0.3713	6608	X-RAY DIFFRACTION	100
2.2026-2.2316	0.3964	334	0.3386	6740	X-RAY DIFFRACTION	100
2.2316-2.2622	0.3338	324	0.3334	6637	X-RAY DIFFRACTION	100
2.2622-2.2945	0.3424	355	0.3191	6537	X-RAY DIFFRACTION	100
2.2945-2.3287	0.3454	347	0.3009	6732	X-RAY DIFFRACTION	100
2.3287-2.3651	0.3249	355	0.2807	6585	X-RAY DIFFRACTION	100
2.3651-2.4039	0.3225	381	0.2789	6565	X-RAY DIFFRACTION	100
2.4039-2.4453	0.2974	351	0.272	6757	X-RAY DIFFRACTION	100
2.4453-2.4898	0.2961	341	0.2602	6605	X-RAY DIFFRACTION	100
2.4898-2.5377	0.2408	306	0.2424	6648	X-RAY DIFFRACTION	100
2.5377-2.5895	0.2586	313	0.232	6771	X-RAY DIFFRACTION	100
2.5895-2.6458	0.2671	320	0.2327	6588	X-RAY DIFFRACTION	100
2.6458-2.7073	0.2219	307	0.2273	6737	X-RAY DIFFRACTION	100
2.7073-2.775	0.2562	331	0.2202	6626	X-RAY DIFFRACTION	100
2.775-2.8501	0.26	362	0.2074	6646	X-RAY DIFFRACTION	100
2.8501-2.9339	0.2615	355	0.2086	6611	X-RAY DIFFRACTION	100
2.9339-3.0286	0.2557	386	0.2081	6676	X-RAY DIFFRACTION	100
3.0286-3.1369	0.2458	320	0.2212	6631	X-RAY DIFFRACTION	100
3.1369-3.2624	0.268	377	0.2178	6658	X-RAY DIFFRACTION	100
3.2624-3.4109	0.2407	374	0.2022	6632	X-RAY DIFFRACTION	100
3.4109-3.5907	0.2133	365	0.1894	6612	X-RAY DIFFRACTION	100
3.5907-3.8156	0.2034	354	0.1821	6622	X-RAY DIFFRACTION	100
3.8156-4.1101	0.198	380	0.1687	6654	X-RAY DIFFRACTION	100
4.1101-4.5236	0.1835	366	0.1461	6629	X-RAY DIFFRACTION	100
4.5236-5.1777	0.1702	383	0.1386	6681	X-RAY DIFFRACTION	100
5.1777-6.5217	0.2123	395	0.1679	6604	X-RAY DIFFRACTION	100
6.5217-54.7539	0.201	340	0.1786	6621	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.7151	0.2077	0.1576	2.3924	-0.0971	2.3066	-0.2511	0.8021	-0.4646	-0.784	0.3359	0.2443	0.6597	-0.5066	-0.0513	0.7148	-0.2787	-0.0257	1.0922	-0.0846	0.5075	18.6063	26.7399	223.1977
2	1.8778	0.2459	-0.6856	1.3695	-0.4632	1.9	-0.0179	0.2248	0.0984	-0.0737	0.0265	-0.1537	-0.1339	0.1486	-0.0291	0.3102	-0.0081	-0.0279	0.624	0.0595	0.3136	38.6274	47.3476	238.0906
3	1.2755	0.5141	-0.359	0.366	-0.2369	1.3475	0.0263	0.1985	0.2082	0.0899	0.1277	0.2028	-0.1367	-0.6752	-0.1729	0.3827	0.0621	0.0016	0.837	0.1183	0.3983	11.8245	42.9355	248.5606
4	1.7305	0.1813	-1.0348	0.9406	0.251	2.778	0.0704	-0.4019	0.1005	0.2388	-0.0666	0.1765	-0.1064	-0.5908	-0.0671	0.4395	0.0082	-0.0071	0.8487	0.1286	0.3643	8.9015	34.2598	271.7171
5	2.1744	0.4013	-0.5164	0.7119	0.3294	1.1222	0.1245	-0.0991	0.339	0.1682	-0.0571	0.1161	-0.3189	-0.5246	-0.0507	0.4516	0.1068	0.0393	0.821	0.1027	0.3435	8.8574	44.4804	270.0346
6	2.8589	-0.5179	-0.8149	1.0548	-0.3951	1.5033	0.0127	-0.6079	0.2677	0.1291	-0.0742	-0.0161	-0.5095	-0.6042	0.2	0.6705	0.152	-0.0438	1.04	-0.146	0.5596	15.3671	49.0006	280.0594
7	3.5162	-0.7052	-0.7318	2.0521	-1.1571	5.0335	-0.4787	-1.1679	0.8729	0.368	-0.1616	-0.3836	-1.1424	0.1716	0.4748	1.0073	0.087	-0.3251	0.9565	-0.1555	0.8201	31.1489	53.8637	285.0167
8	0.7852	-0.7118	-0.397	2.0045	0.9723	1.0735	-0.1006	-0.404	0.3576	-0.0048	-0.0166	0.1692	-0.4164	-0.0946	0.132	0.4996	-0.0151	0.0012	0.6551	-0.1031	0.4137	12.7814	29.9605	317.002
9	3.1397	0.3152	0.4582	3.1107	0.8884	3.6666	0.089	-0.3332	0.3464	0.286	-0.0621	0.023	-0.4548	0.0123	-0.0524	0.4688	0.0119	0.0101	0.7298	-0.1387	0.3548	19.5914	29.5448	322.5013
10	2.4129	-0.5578	-1.0199	1.8905	1.3329	3.5572	-0.0033	-0.1838	0.1239	-0.0543	0.016	0.0173	-0.1803	-0.2186	0.0368	0.349	-0.0376	-0.0135	0.562	-0.0303	0.3213	19.8574	20.7594	308.5637
11	3.1812	0.0588	0.1548	2.0794	-0.0054	1.6728	-0.0079	-0.026	-0.4633	0.0119	0.0271	-0.4777	0.285	0.408	-0.0193	0.4088	-0.0002	0.0118	0.6483	-0.0347	0.477	38.4426	5.9453	302.1257
12	1.7022	-0.2525	0.1504	1.8529	-0.5288	1.9832	-0.0045	0.0428	-0.2102	-0.0998	0.1288	0.0689	0.2976	-0.3282	-0.1262	0.3341	-0.1102	0.0013	0.5243	-0.0201	0.2852	16.297	8.2494	296.4857
13	4.6341	0.6505	0.5866	2.8109	0.5571	1.5847	-0.1357	0.3518	-0.1019	0.0153	0.116	0.7403	0.2442	-0.6901	-0.0043	0.5084	-0.1733	-0.0034	1.1068	0.0871	0.4696	-0.7225	17.0294	278.2836
14	1.6157	0.1369	0.654	1.7724	0.4158	1.7035	-0.0714	0.3704	-0.0495	-0.3775	0.087	0.2361	0.2384	-0.545	0.0122	0.5386	-0.1856	-0.0046	0.9299	0.0893	0.3749	8.5629	19.1901	268.3245
15	1.8322	-0.3268	1.3407	0.9629	0.1221	1.75	0.1087	0.4638	-0.438	-0.4976	-0.0126	0.1723	0.5675	-0.4109	-0.1355	0.7585	-0.2442	-0.0579	0.945	-0.0606	0.4239	9.5099	8.0758	265.3772
16	3.0789	-0.8251	0.0399	1.6074	-0.6057	0.4528	0.1621	0.6399	0.1424	-0.259	-0.0527	-0.6233	0.2326	-0.0056	-0.0135	1.1911	-0.1126	0.0665	1.3057	-0.1535	0.7686	28.8239	0.9104	255.4142

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 142 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 143 THROUGH 308 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 309 THROUGH 488 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 489 THROUGH 544 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 545 THROUGH 579 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 580 THROUGH 616 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 617 THROUGH 715 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 2 THROUGH 34 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 35 THROUGH 96 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 97 THROUGH 142 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 143 THROUGH 308 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 309 THROUGH 440 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 441 THROUGH 488 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 489 THROUGH 544 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 545 THROUGH 610 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 611 THROUGH 714 )

-
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 , 2 types, 2 molecules AB

-
Non-polymers , 4 types, 323 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 , 2 types, 2 molecules AB

-Non-polymers , 4 types, 323 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 , 2 types, 2 molecules AB

-
Non-polymers , 4 types, 323 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