PDB-5q0c: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph...

ID or keywords:

Entry

Database: PDB / ID: 5q0c

Title

Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-[5-(4-methoxyphenyl)thiophen-2-yl]sulfonylurea and with fructose-2,6-diphosphate

Components

Fructose-1,6-bisphosphatase isozyme 2

Keywords

HYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Gluconeogenesis / Fructose-1-6-bisphosphatase active site. / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase class I, N-terminal /

Fructose-1,6-bisphosphatase /

Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase class 1 / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate metabolic process ...

Function and homology information

Specimen source

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / 2.4 Å resolution

Model details

For D3R project

Authors

Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.

Citation

Journal: To be published
Title: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(5-bromo-1,3-thiazol-2-yl)-3-[5-(4-methoxyphenyl)thiophen-2-yl]sulfonylurea and with f2,6p
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.

Validation Report

Summary

Full report

About validation report

Date

Deposition: Apr 18, 2017 / Release: Jan 9, 2019

Revision	Date	Data content type	Group	Category	Item	Provider	Type
1.0	Jan 9, 2019	Structure model				repository	Initial release
1.1	Jan 16, 2019	Structure model	Data collection	diffrn_radiation	_diffrn_radiation.pdbx_diffrn_protocol
1.2	Feb 6, 2019	Structure model	Data collection / Database references / Structure summary	audit_author / citation_author	_audit_author.name / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmcif format	5q0c.cif.gz / Display in browser / Tree view / PDBx/mmCIF dictionary
PDB format	pdb5q0c.ent.gz / Display in browser / PDB Contents Guide
PDBML Plus	5q0c-add.xml.gz / Display in browser*PLUS
Others	Other downloads

-
Links

PDB pages	PDBj / RCSB PDB / PDBe / NCBI

-
Related structure data

Similar-shape strucutres	Search similar-shape structures by Omokage search Omokage search

Deposited unit

A: Fructose-1,6-bisphosphatase isozyme 2

B: Fructose-1,6-bisphosphatase isozyme 2

C: Fructose-1,6-bisphosphatase isozyme 2

D: Fructose-1,6-bisphosphatase isozyme 2

E: Fructose-1,6-bisphosphatase isozyme 2

F: Fructose-1,6-bisphosphatase isozyme 2

G: Fructose-1,6-bisphosphatase isozyme 2

H: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

301 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fructose-1,6-bisphosphatase isozyme 2

B: Fructose-1,6-bisphosphatase isozyme 2

C: Fructose-1,6-bisphosphatase isozyme 2

D: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

defined by author&software
150 kDa, 4 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Fructose-1,6-bisphosphatase isozyme 2

F: Fructose-1,6-bisphosphatase isozyme 2

G: Fructose-1,6-bisphosphatase isozyme 2

H: Fructose-1,6-bisphosphatase isozyme 2

hetero molecules

defined by author&software
150 kDa, 4 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

γ

α

β

Length a, b, c (Å)	222.475, 240.518, 138.979
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C 2 2 21

#1: Protein/peptide	Fructose-1,6-bisphosphatase isozyme 2 / FBPase 2 / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase 2 / Muscle FBPase Mass: 36798.094 Da / Num. of mol.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00757, fructose-bisphosphatase
#2: Chemical	ChemComp-96G / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-5-(4-methoxyphenyl)thiophene-2-sulfonamide Mass: 474.372 Da / Num. of mol.: 8 / Formula: C₁₅H₁₂BrN₃O₄S₃
#3: Chemical	ChemComp-FDP / FRUCTOSE-2,6-DIPHOSPHATE Mass: 340.116 Da / Num. of mol.: 8 / Formula: C₆H₁₄O₁₂P₂ / Fructose 2,6-bisphosphate
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 545 / Formula: H₂O / Water

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.26 / Density percent sol: 62.3 %
Crystal grow	Method: vapor diffusion, sitting drop Details: entry deposited much later from experimental date, thus exact crystallization details not known

-
Data collection

Diffraction	Mean temperature: 100
Source	Source: SYNCHROTRON / Type: SLS BEAMLINE X10SA / Synchrotron site: SLS / Beamline: X10SA / Wavelength: 0.987
Detector	Type: MAR CCD 165 mm / Detector: CCD / Collection date: Jun 12, 2006
Radiation	Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 / Relative weight: 1
Reflection	D resolution high: 2.4 / D resolution low: 29.793 / Number obs: 141184 / Percent possible obs: 97.51

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Language: C++ / Type: package

Name	Version	Classification	Contact author	Contact author email	Location	Date
PHENIX	1.11.1_2575	refinement	Paul D. Adams	PDAdams[at]lbl.gov	http://www.phenix-online.org/
PDB_EXTRACT	3.23	data extraction	PDB	deposit[at]deposit.rcsb.org	http://sw-tools.pdb.org/apps/PDB_EXTRACT/	Dec. 13, 2016

Refine

Method to determine structure:

MOLECULAR REPLACEMENT / Overall SU ML: 0.28 / Cross valid method: THROUGHOUT / Sigma F: 1.34 / Overall phase error: 23.83 / Stereochemistry target values: ML

Solvent computation

Solvent shrinkage radii: 0.9 / Solvent vdw probe radii: 1.11 / Solvent model details: FLAT BULK SOLVENT MODEL

Displacement parameters

B iso max: 185.73 / B iso mean: 57.1469 / B iso min: 17.1

Least-squares process

R factor R free: 0.2103 / R factor R work: 0.1682 / R factor obs: 0.1703 / Highest resolution: 2.4 / Lowest resolution: 29.793 / Number reflection R free: 6943 / Number reflection R work: 134241 / Number reflection obs: 141184 / Percent reflection R free: 4.92 / Percent reflection obs: 97.51

Refine hist #final

Highest resolution: 2.4 / Lowest resolution: 29.793 / B iso mean ligand: 66.91 / B iso mean solvent: 48.99 / Number residues total: 2618

Number of atoms included #final

Protein: 19932 / Nucleic acid: 0 / Ligand: 368 / Solvent: 545 / Total: 20845

Refine LS restraints

Refine ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	20627
X-RAY DIFFRACTION	f_angle_d	0.960	27954
X-RAY DIFFRACTION	f_chiral_restr	0.057	3225
X-RAY DIFFRACTION	f_plane_restr	0.006	3519
X-RAY DIFFRACTION	f_dihedral_angle_d	11.223	12388

Refine LS restraints ncs

Ens ID: 1 / Number: 12348 / Refine ID: X-RAY DIFFRACTION / Rms: 5.692 / Type: TORSIONAL

Dom ID	Auth asym ID
1	A
2	B
3	C
4	D
5	E
6	F
7	G
8	H

Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolution	R factor R free	R factor R work	Lowest resolution	Number reflection R free	Number reflection R work	Number reflection all	Percent reflection obs
2.4000	0.3007	0.2528	2.4273	186	3598	3784	79.0000
2.4273	0.3147	0.2380	2.4558	201	3776	3977	83.0000
2.4558	0.2771	0.2326	2.4857	201	3918	4119	86.0000
2.4857	0.3014	0.2275	2.5172	228	4136	4364	91.0000
2.5172	0.3069	0.2290	2.5503	206	4326	4532	95.0000
2.5503	0.2740	0.2166	2.5852	204	4558	4762	99.0000
2.5852	0.2614	0.2058	2.6221	247	4535	4782	99.0000
2.6221	0.2720	0.2118	2.6612	243	4471	4714	99.0000
2.6612	0.2587	0.2084	2.7028	249	4522	4771	99.0000
2.7028	0.2696	0.2033	2.7471	212	4562	4774	100.0000
2.7471	0.2912	0.1961	2.7944	240	4543	4783	100.0000
2.7944	0.2321	0.1928	2.8452	259	4518	4777	100.0000
2.8452	0.2676	0.2022	2.8999	253	4551	4804	100.0000
2.8999	0.2709	0.2128	2.9590	230	4572	4802	100.0000
2.9590	0.2601	0.2188	3.0233	232	4588	4820	100.0000
3.0233	0.2593	0.2068	3.0936	227	4564	4791	100.0000
3.0936	0.3011	0.2087	3.1708	219	4585	4804	100.0000
3.1708	0.2350	0.2043	3.2565	232	4561	4793	100.0000
3.2565	0.2595	0.2052	3.3522	220	4576	4796	100.0000
3.3522	0.2381	0.2043	3.4602	234	4572	4806	100.0000
3.4602	0.2375	0.1877	3.5837	223	4622	4845	100.0000
3.5837	0.2131	0.1641	3.7269	230	4569	4799	100.0000
3.7269	0.1978	0.1546	3.8962	247	4600	4847	100.0000
3.8962	0.1811	0.1438	4.1011	251	4579	4830	100.0000
4.1011	0.1712	0.1293	4.3573	233	4604	4837	100.0000
4.3573	0.1473	0.1160	4.6926	224	4641	4865	100.0000
4.6926	0.1494	0.1160	5.1626	237	4633	4870	100.0000
5.1626	0.1606	0.1303	5.9046	255	4629	4884	100.0000
5.9046	0.1937	0.1549	7.4201	248	4701	4949	100.0000
7.4201	0.1643	0.1443	29.7949	272	4631	4903	96.0000

Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

ID	L11	L12	L13	L22	L23	L33	S11	S12	S13	S21	S22	S23	S31	S32	S33	T11	T12	T13	T22	T23	T33	Origin x	Origin y	Origin z
1	0.1763	0.0571	-0.1484	0.0290	-0.0575	0.0807	0.1527	-0.2064	0.0696	0.0768	-0.1680	-0.0181	0.0294	0.0412	-0.0000	0.3562	-0.0176	0.0114	0.3753	-0.0959	0.3755	53.9468	5.5753	-23.6298
2	0.0153	-0.0003	-0.0186	0.0223	-0.0358	0.0596	0.0483	-0.3837	-0.0872	-0.1044	-0.0363	-0.2333	0.0992	0.0217	-0.0000	0.3736	-0.0282	-0.0438	0.5065	-0.0662	0.3151	47.4790	2.3112	-10.4508
3	0.5645	-0.2037	-0.2250	0.1693	-0.0124	0.4285	0.0643	-0.1169	0.0964	-0.0338	0.0035	0.0478	-0.0677	-0.0331	0.0018	0.2319	0.0062	0.0119	0.2675	-0.0770	0.1947	31.3604	9.8582	-23.7315
4	0.1994	-0.0306	0.1327	0.0193	0.0181	0.0234	0.1055	0.1454	-0.0073	-0.1336	-0.0576	-0.0774	-0.0732	0.0599	0.0000	0.3203	0.0095	0.0043	0.3364	-0.1041	0.3378	53.5315	-7.7661	-45.7173
5	-0.0018	0.0053	0.0200	0.0088	0.0213	0.0407	-0.0715	0.2336	-0.0291	-0.1609	-0.0097	-0.2075	-0.1201	0.1094	0.0000	0.4160	0.0380	0.0048	0.4177	-0.1001	0.2948	47.3425	-4.1490	-58.9784
6	0.1903	-0.0047	0.0492	0.2263	0.1222	0.3685	0.0428	0.1131	-0.0993	-0.0293	-0.0406	0.1059	0.0350	-0.1037	-0.0000	0.3342	-0.0087	-0.0563	0.3569	-0.0926	0.3408	30.6861	-10.5385	-45.7219
7	0.2092	0.1416	-0.1048	0.0806	-0.0474	0.0376	0.0745	-0.0310	0.1622	-0.0160	-0.0362	0.0566	-0.0112	0.0954	-0.0000	0.3285	-0.0051	-0.0103	0.3710	-0.1263	0.3869	65.2184	10.2867	-29.5140
8	0.0044	-0.0049	0.0285	0.0438	-0.0268	0.0466	0.0804	0.1703	0.5533	-0.0937	-0.0881	-0.0968	-0.1538	-0.1023	0.0001	0.4111	0.0212	0.0230	0.4396	-0.0306	0.6250	72.1137	22.7072	-34.5162
9	0.3837	0.0417	-0.0325	0.1789	-0.0722	0.3355	0.1006	-0.0438	0.1280	0.0820	-0.1188	-0.1183	-0.0103	-0.0025	-0.0000	0.3116	-0.0263	-0.0524	0.3031	-0.0305	0.3753	87.9275	9.7744	-25.8999
10	0.0509	0.0093	-0.0032	0.0226	-0.0011	0.0037	0.0952	0.1315	-0.2201	0.0038	-0.0855	0.0099	0.0947	0.0766	-0.0000	0.3332	0.0217	-0.0340	0.4065	-0.1101	0.3456	64.2748	-16.6111	-49.0986
11	0.0538	0.0110	-0.0144	0.0676	-0.0839	0.0888	-0.0001	-0.0262	-0.2435	0.1287	-0.1620	0.0874	0.0922	-0.1418	0.0001	0.3734	-0.0320	0.0035	0.3120	-0.0205	0.4045	68.1892	-21.5489	-31.3993
12	0.2129	0.0754	0.0957	0.3543	0.2745	0.3384	-0.0008	0.0532	-0.1295	0.0762	-0.0136	-0.1351	0.0731	0.0344	0.0000	0.2903	0.0497	-0.0164	0.3052	-0.0418	0.3667	87.0389	-14.5522	-43.2537
13	0.1633	-0.0936	-0.1520	0.4937	-0.0205	0.1132	-0.1222	-0.1806	0.2454	0.0269	0.1046	0.8178	-0.3018	-0.0565	-0.0573	0.3434	-0.0414	-0.2379	0.3674	0.1447	0.7183	94.6678	53.5036	-1.9141
14	0.5262	-0.0059	-0.4329	0.5589	0.3060	0.6128	-0.4902	-0.0751	-0.0569	-0.1491	0.3093	0.7287	0.3305	0.2053	-0.2193	0.3469	-0.2601	-0.3324	0.2294	0.0596	0.4140	99.7458	33.9017	-8.4156
15	0.0484	-0.0957	0.0213	0.2309	0.0305	0.0301	-0.1091	0.0355	0.1687	-0.1208	0.0562	-0.2369	-0.0625	-0.0452	0.0000	0.4631	-0.0255	-0.1214	0.3800	0.0099	0.3997	124.7628	56.8741	2.9868
16	0.0308	-0.0298	-0.0193	0.0148	0.0169	0.0377	-0.1019	0.0830	0.0380	-0.2863	0.0655	-0.4062	-0.2782	0.0983	0.0000	0.4712	-0.0432	0.0066	0.4413	0.0556	0.4987	136.8292	50.9761	-3.6256
17	0.2742	-0.0941	-0.0073	0.3725	-0.0043	0.1462	-0.0912	0.0124	-0.0314	-0.0237	0.0304	-0.1204	0.0768	-0.0015	0.0000	0.3863	0.0178	-0.0488	0.3256	0.0356	0.3305	125.9816	34.1882	5.9424
18	0.1180	-0.0047	-0.0661	0.3771	0.2568	0.2959	-0.1017	-0.0052	-0.0471	-0.5805	0.1835	0.0945	0.1372	0.1116	0.1697	0.5117	-0.0619	-0.2810	0.3609	0.1010	0.4685	104.7034	67.8393	-11.0772
19	0.1086	-0.0689	0.0710	0.0375	-0.0479	0.0410	0.0547	0.1727	-0.2540	-0.7995	-0.0235	0.3028	0.0288	-0.1801	0.0778	1.0568	-0.0505	-0.6068	0.4660	0.0939	0.1953	106.8581	74.3508	-24.3700
20	0.2012	-0.2263	0.0926	0.4930	-0.2932	0.4178	0.0099	-0.1090	-0.0080	-0.2795	0.1340	0.4650	-0.0292	-0.0579	0.4520	0.4008	0.0019	-0.2247	0.3774	0.1194	0.4199	100.8624	90.5397	-10.3169
21	0.0334	-0.0103	0.0394	0.2338	0.0213	0.0287	-0.0442	-0.0809	-0.0554	0.1011	0.1487	0.0743	0.1682	0.0476	0.0001	0.3353	0.0104	-0.1115	0.3471	0.0287	0.3828	120.0315	67.7865	9.6452
22	0.0082	-0.0078	-0.0068	0.0279	0.0228	0.0334	-0.0642	-0.1781	-0.1661	0.3626	0.0226	0.0246	0.0764	0.0370	-0.0000	0.5129	0.0187	-0.0994	0.4821	0.0497	0.3267	117.7942	73.6441	23.2512
23	0.1735	-0.0810	0.1312	0.4114	0.0718	0.4121	-0.0505	-0.0228	0.0466	0.1002	0.0898	-0.0975	-0.0497	0.0192	-0.0000	0.3268	-0.0041	-0.0804	0.3715	-0.0081	0.3061	123.0566	90.5463	9.8381

Refine TLS group

Refine ID: X-RAY DIFFRACTION

ID	Beg auth asym ID	Beg auth seq ID	End auth asym ID	End auth seq ID	Refine TLS ID	Selection details
1	A	9	A	69	1	chain 'A' and (resid 9 through 69 )
2	A	70	A	119	2	chain 'A' and (resid 70 through 119 )
3	A	120	A	336	3	chain 'A' and (resid 120 through 336 )
4	B	9	B	69	4	chain 'B' and (resid 9 through 69 )
5	B	70	B	119	5	chain 'B' and (resid 70 through 119 )
6	B	120	B	336	6	chain 'B' and (resid 120 through 336 )
7	C	9	C	69	7	chain 'C' and (resid 9 through 69 )
8	C	70	C	119	8	chain 'C' and (resid 70 through 119 )
9	C	120	C	336	9	chain 'C' and (resid 120 through 336 )
10	D	9	D	49	10	chain 'D' and (resid 9 through 49 )
11	D	50	D	119	11	chain 'D' and (resid 50 through 119 )
12	D	120	D	336	12	chain 'D' and (resid 120 through 336 )
13	E	9	E	119	13	chain 'E' and (resid 9 through 119 )
14	E	120	E	336	14	chain 'E' and (resid 120 through 336 )
15	F	9	F	69	15	chain 'F' and (resid 9 through 69 )
16	F	70	F	119	16	chain 'F' and (resid 70 through 119 )
17	F	120	F	336	17	chain 'F' and (resid 120 through 336 )
18	G	9	G	69	18	chain 'G' and (resid 9 through 69 )
19	G	70	G	119	19	chain 'G' and (resid 70 through 119 )
20	G	120	G	336	20	chain 'G' and (resid 120 through 336 )
21	H	9	H	69	21	chain 'H' and (resid 9 through 69 )
22	H	70	H	119	22	chain 'H' and (resid 70 through 119 )
23	H	120	H	336	23	chain 'H' and (resid 120 through 336 )

-
News

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

+
Aug 31, 2016. New EM Navigator & Yorodumi

-
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.

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

-
Links

-
Related structure data

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

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

-
Jul 12, 2017. Major update of PDB

+
Jun 16, 2017. Omokage search with filter

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

+
Aug 31, 2016. New EM Navigator & Yorodumi

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

+Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Links

-Related structure data

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

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

-Jul 12, 2017. Major update of PDB

+Jun 16, 2017. Omokage search with filter

+Sep 15, 2016. EM Navigator & Yorodumi renewed

+Aug 31, 2016. New EM Navigator & Yorodumi

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

+
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Links

-
Related structure data

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

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

-
Jul 12, 2017. Major update of PDB

+
Jun 16, 2017. Omokage search with filter

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

+
Aug 31, 2016. New EM Navigator & Yorodumi

-
Yorodumi