[English] 日本語
Yorodumi
- PDB-5q08: Human liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosph... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5q08
TitleHuman liver fructose-1,6-bisphosphatase 1 (fructose 1,6-bisphosphate 1-phosphatase, E.C.3.1.3.11) complexed with the allosteric inhibitor 1-(1-benzothiophen-3-ylsulfonyl)-3-(5-bromo-1,3-thiazol-2-yl)urea
ComponentsFructose-1,6-bisphosphatase 1Fructose 1,6-bisphosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / D3R docking / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyFructose-1,6-bisphosphatase class 1 / Fructose-1,6-bisphosphatase, active site / Fructose-1,6-bisphosphatase / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase active site. / fructose 1,6-bisphosphate 1-phosphatase activity / carbohydrate metabolic process / Fructose-1,6-bisphosphatase 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.2 Å resolution
Model detailsFor D3R project
AuthorsRuf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G. / Yang, H. / Shao, C. / Burley, S.K.
CitationJournal: 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-(1-benzothiophen-3-ylsulfonyl)-3-(5-bromo-1,3-thiazol-2-yl)urea
Authors: Ruf, A. / Joseph, C. / Alker, A. / Banner, D. / Tetaz, T. / Benz, J. / Kuhn, B. / Rudolph, M.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 18, 2017 / Release: Jan 9, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 9, 2019Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collectiondiffrn_radiation_diffrn_radiation.pdbx_diffrn_protocol
1.2Feb 6, 2019Structure modelData collection / Database references / Structure summaryaudit_author / citation_author_audit_author.name / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,22216
Polyers294,8758
Non-polymers3,3468
Water23,7981321
1
A: Fructose-1,6-bisphosphatase 1
B: Fructose-1,6-bisphosphatase 1
C: Fructose-1,6-bisphosphatase 1
D: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1118
Polyers147,4384
Non-polymers1,6734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15860
ΔGint (kcal/M)-81
Surface area (Å2)44490
MethodPISA
2
E: Fructose-1,6-bisphosphatase 1
F: Fructose-1,6-bisphosphatase 1
G: Fructose-1,6-bisphosphatase 1
H: Fructose-1,6-bisphosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1118
Polyers147,4384
Non-polymers1,6734
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)15790
ΔGint (kcal/M)-82
Surface area (Å2)44010
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)66.220, 285.134, 83.359
Angle α, β, γ (deg.)90.000, 97.570, 90.000
Int Tables number4
Space group name H-MP 1 21 1

-
Components

#1: Protein/peptide
Fructose-1,6-bisphosphatase 1 / Fructose 1,6-bisphosphatase / Growth-inhibiting protein 17 / cDNA FLJ75786 / highly similar to Homo sapiens fructose-1 / 6-bisphosphatase 1 (FBP1) / mRNA


Mass: 36859.418 Da / Num. of mol.: 8 / Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, hCG_1640493 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TU34, fructose-bisphosphatase
#2: Chemical
ChemComp-967 / N-[(5-bromo-1,3-thiazol-2-yl)carbamoyl]-1-benzothiophene-3-sulfonamide


Mass: 418.309 Da / Num. of mol.: 8 / Formula: C12H8BrN3O3S3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1321 / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.73 / Density percent sol: 54.99 %
Crystal growTemp: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES pH 7.0, 0.1M AMMONIUM ACETATE, 12%-25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X10SA / Synchrotron site: SLS / Beamline: X10SA / Wavelength: 0.987
DetectorType: MAR CCD 165 mm / Detector: CCD / Collection date: Dec 8, 2006
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionD resolution high: 2.2 Å / D resolution low: 29.213 Å / Number obs: 153919 / Percent possible obs: 99.79

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software

Language: C++ / Type: package

NameVersionClassificationContact authorContact author emailLocationDate
PHENIX1.11.1_2575refinementPaul D. AdamsPDAdams[at]lbl.govhttp://www.phenix-online.org/
PDB_EXTRACT3.23data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/Dec. 13, 2016
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.25 / Cross valid method: THROUGHOUT / Sigma F: 1.35 / Overall phase error: 20.85 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 142.77 Å2 / B iso mean: 37.7687 Å2 / B iso min: 8.79 Å2
Least-squares processR factor R free: 0.2045 / R factor R work: 0.1575 / R factor obs: 0.1599 / Highest resolution: 2.2 Å / Lowest resolution: 29.213 Å / Number reflection R free: 7746 / Number reflection R work: 146173 / Number reflection obs: 153919 / Percent reflection R free: 5.03 / Percent reflection obs: 99.79
Refine hist #finalHighest resolution: 2.2 Å / Lowest resolution: 29.213 Å / B iso mean ligand: 39.25 / B iso mean solvent: 42.02 / Number residues total: 2542
Number of atoms included #finalProtein: 19456 / Nucleic acid: 0 / Ligand: 176 / Solvent: 1321 / Total: 20953
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820062
X-RAY DIFFRACTIONf_angle_d0.93627117
X-RAY DIFFRACTIONf_chiral_restr0.0583062
X-RAY DIFFRACTIONf_plane_restr0.0063461
X-RAY DIFFRACTIONf_dihedral_angle_d11.38312175
Refine LS restraints ncs

Ens ID: 1 / Number: 12116 / Refine ID: X-RAY DIFFRACTION / Rms: 8.572 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2B
3C
4D
5E
6F
7G
8H
Refine LS shell

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

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.20000.33010.27552.22502514568481994.0000
2.22500.28600.23072.251224349035146100.0000
2.25120.28540.21782.278625848645122100.0000
2.27860.25190.20342.307431048495159100.0000
2.30740.27570.19052.337824848465094100.0000
2.33780.23660.18452.369825349365189100.0000
2.36980.24160.17802.403626248225084100.0000
2.40360.23460.17892.439525149065157100.0000
2.43950.25610.18312.477626248415103100.0000
2.47760.25040.18242.518226748815148100.0000
2.51820.26520.18252.561627448865160100.0000
2.56160.24780.17892.608225148425093100.0000
2.60820.23660.17022.658325649015157100.0000
2.65830.23120.16452.712524148845125100.0000
2.71250.23820.16442.771424849335181100.0000
2.77140.21760.15832.835924448625106100.0000
2.83590.20690.15232.906729148355126100.0000
2.90670.21740.15532.985227048835153100.0000
2.98520.21030.15343.073024248825124100.0000
3.07300.20050.15183.172124549125157100.0000
3.17210.20420.15283.285323149065137100.0000
3.28530.21370.15463.416625948915150100.0000
3.41660.20840.14793.571923848805118100.0000
3.57190.17450.14133.759828248815163100.0000
3.75980.18230.13863.994827148745145100.0000
3.99480.15160.13214.302425348915144100.0000
4.30240.14620.11904.733728349165199100.0000
4.73370.16580.13095.414923548915126100.0000
5.41490.19890.16676.808026048925152100.0000
6.80800.18770.161429.21512674915518299.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.23820.02830.06850.15130.04310.1490-0.0918-0.03950.0336-0.2522-0.0257-0.0463-0.03320.0665-0.06890.24310.00370.01900.15030.04180.188337.660715.9894-5.5378
20.0525-0.0267-0.00450.0334-0.00660.0896-0.05950.03650.0621-0.28840.01090.1245-0.08810.0116-0.00830.31160.0409-0.08450.17320.02700.258720.094722.8678-7.8307
30.00890.0132-0.01640.0266-0.01810.05430.0261-0.01090.1058-0.12380.01450.0629-0.0771-0.02690.06610.41060.1731-0.2489-0.11700.21790.134718.404831.3729-10.1902
40.00140.00260.00130.0199-0.00670.0072-0.0406-0.0305-0.00630.08620.03850.0112-0.04160.03140.00100.12510.01900.04140.37050.03290.250322.16820.852131.3703
50.0063-0.0331-0.00130.16440.01580.0039-0.0103-0.0537-0.0565-0.0849-0.06640.14470.0492-0.0483-0.01400.1224-0.00210.00740.20960.00930.270515.9072-3.17998.8910
60.0492-0.01280.03270.12430.03810.0457-0.00800.0017-0.0414-0.0503-0.11460.1516-0.0055-0.0382-0.08950.0835-0.02520.03330.25280.02110.39335.1162-1.588013.4673
70.00190.00100.00260.00030.00030.0045-0.0319-0.0044-0.04650.02560.00060.04650.0314-0.0164-0.00470.07460.02460.17150.28880.00900.39121.9811-1.374923.6676
80.01350.00070.02090.01250.01860.0973-0.0768-0.0726-0.01410.05200.05630.1345-0.0877-0.0165-0.00530.12890.04360.03020.19610.00370.230814.379811.531420.0825
90.0325-0.0382-0.01170.04520.00340.00820.01950.03080.01730.03340.01630.0578-0.1153-0.00490.00420.26760.1233-0.02940.2612-0.05230.45563.523832.21569.8314
100.01930.0004-0.02730.02990.02320.1751-0.0254-0.0457-0.08110.00080.05360.2777-0.1427-0.13060.02820.03790.11990.00810.2621-0.04370.51301.277719.038717.7465
110.0027-0.0030-0.00220.00490.00110.00570.0035-0.02170.0439-0.0712-0.0078-0.0526-0.0102-0.0224-0.00020.3715-0.01900.08820.22720.04310.199447.38486.4596-14.7529
120.00350.00590.00570.00510.00790.00780.02770.0594-0.0947-0.1444-0.03880.1356-0.0013-0.0688-0.00000.17320.02660.00330.19350.00550.173331.4678-9.2087-6.7400
130.05210.01960.00620.01770.01160.0051-0.00340.0388-0.13830.00980.06120.03990.0436-0.00810.02640.25680.05550.02740.19180.04520.085436.4182-15.9642-15.0879
140.0025-0.0002-0.0005-0.0008-0.00070.00180.0579-0.0100-0.0564-0.0948-0.04780.05340.0042-0.00540.00000.29920.05730.03190.21760.02450.135543.1094-13.7981-22.7796
150.04300.04690.02320.09070.03060.02800.03400.04820.0830-0.1433-0.0217-0.0617-0.01490.1177-0.02910.15860.01140.05470.20360.02740.161450.0075-8.8777-6.8183
160.0110-0.00540.01670.0074-0.01100.0589-0.10820.0611-0.0683-0.0336-0.0979-0.07370.05050.0250-0.00750.18200.07750.05360.23700.02850.258761.6079-28.85084.0323
170.01390.00460.01240.00040.00090.01430.01830.0131-0.0404-0.02200.0392-0.06950.1201-0.0414-0.00000.25070.01750.04010.23430.02120.200651.8023-21.0426-6.4100
180.00840.02380.00580.07540.02580.0129-0.03470.0073-0.0423-0.1923-0.0562-0.05730.08970.0574-0.01810.18280.05680.09200.2564-0.00100.212559.6677-24.6368-11.3742
190.0217-0.0522-0.00180.0945-0.00560.0422-0.0125-0.04610.06290.09970.03790.0205-0.0378-0.03610.00050.15510.02100.03440.20640.01660.144836.2416-4.764024.9468
200.06210.03270.03080.1863-0.02010.0965-0.0044-0.0240-0.01580.1045-0.00960.01730.12730.0059-0.03610.13710.02260.01510.13390.04580.103142.0381-21.997819.7232
210.0293-0.0069-0.02500.0123-0.00420.0154-0.0414-0.08300.01610.03980.0352-0.00770.04760.0570-0.00010.16860.0508-0.00500.17780.03700.126947.6563-27.023024.6716
220.10690.01510.01650.0146-0.00820.01030.0717-0.0333-0.19530.1200-0.0085-0.08580.03350.0490-0.00410.26370.0281-0.05940.15990.04040.2580-0.608651.426342.6937
230.1016-0.0689-0.06000.04130.03730.03270.0104-0.0483-0.28940.0941-0.0638-0.04860.09120.0024-0.10550.3479-0.0112-0.08060.17850.12460.3689-4.801442.267345.8798
240.02870.0425-0.05280.1079-0.12190.13730.0361-0.1161-0.26140.07320.07720.1055-0.0405-0.11710.03540.1471-0.0382-0.01360.20520.05300.4313-24.931345.091838.9717
250.0098-0.0144-0.01060.0342-0.01360.13660.0833-0.0412-0.24610.1343-0.0207-0.02350.1448-0.13110.06430.2928-0.0808-0.05460.19920.09950.5549-20.679935.478243.1111
260.06390.0398-0.01710.0736-0.05330.04680.03370.15720.02250.00580.04510.0619-0.1450-0.05740.01320.18650.0443-0.04330.2506-0.00290.1873-18.261069.546116.3170
270.12560.0372-0.03100.0130-0.01110.15010.02630.2960-0.2662-0.0495-0.05540.1237-0.0685-0.1036-0.01500.10620.0053-0.06730.2514-0.13260.3319-22.217851.118815.2452
280.01850.0215-0.00730.0589-0.01390.0131-0.00630.2066-0.18330.02950.08990.12650.0219-0.08410.06660.17920.0161-0.06410.3689-0.14420.4185-29.786447.973511.8767
290.0106-0.0051-0.00440.0057-0.00250.00640.0350-0.0164-0.03630.06920.0262-0.0246-0.00620.00420.00120.41410.0315-0.02520.20230.04040.22236.929559.616254.9658
300.01160.00500.00070.00690.01040.01180.0806-0.07210.03230.02350.00350.0537-0.0229-0.08390.00010.2576-0.00550.01510.18850.00310.1822-6.381475.672543.1572
310.00980.0019-0.00080.01630.01560.01070.0076-0.05140.0640-0.01490.02360.0684-0.0065-0.0226-0.00010.2471-0.03920.02110.17880.01440.1327-3.527682.192452.6010
320.0005-0.00210.00140.0024-0.00260.00230.0409-0.05840.06830.0756-0.06930.0540-0.0011-0.01090.00010.3441-0.0585-0.00740.2396-0.02290.16371.171079.612661.8497
330.0038-0.0072-0.00340.0120-0.00430.00480.0285-0.1142-0.04360.0458-0.0261-0.0180-0.0021-0.01740.00000.2760-0.0271-0.00130.23050.01130.10046.282380.416555.3875
340.0154-0.0150-0.01300.01390.01570.00820.0468-0.03250.01130.0241-0.1084-0.05340.08660.1172-0.00000.24060.0129-0.04220.20810.03520.178014.177872.242344.5803
350.0035-0.01020.00270.0125-0.00220.0062-0.0486-0.0422-0.06190.0426-0.1295-0.0693-0.02440.1043-0.00040.2009-0.0570-0.01860.28480.01150.237025.840094.795040.7603
360.0050-0.0092-0.00590.00280.00400.01490.0967-0.05810.05170.0959-0.0275-0.0637-0.13520.04110.00000.2599-0.02750.00860.2130-0.00040.171813.609787.034148.2591
370.00590.00810.00130.00220.00150.0095-0.0199-0.0442-0.02870.1522-0.0803-0.0040-0.13120.0308-0.00010.2566-0.0810-0.04490.2358-0.00120.165919.914590.520555.1335
380.0071-0.00140.00390.00220.00100.00190.00190.07330.0349-0.01960.02410.0435-0.0142-0.0242-0.00010.2971-0.0072-0.04260.44060.02310.2015-8.939679.85198.0477
390.00590.0135-0.00060.01390.00200.0030-0.00910.0510-0.0578-0.05250.0298-0.01770.07230.02270.00000.21810.0175-0.00580.1859-0.01320.15717.410867.134420.4664
400.00750.0024-0.00790.0066-0.00470.00860.0414-0.0045-0.0996-0.0343-0.0552-0.09340.03730.04910.00000.3665-0.00160.00120.3275-0.01050.165913.923971.65037.7124
410.00730.0081-0.00100.0204-0.00550.00220.0361-0.0399-0.0643-0.0423-0.0169-0.10140.01020.03610.00010.37630.00280.03790.28630.00940.178514.680178.047810.6911
420.0329-0.0119-0.01380.01940.00650.00080.02670.11010.0346-0.08160.01110.0386-0.03500.04300.00000.21190.0128-0.00250.15590.01900.12162.455886.151020.0102
430.00740.0041-0.00150.0008-0.00210.0001-0.0740-0.0189-0.0368-0.0582-0.0504-0.0558-0.06080.0251-0.00010.2544-0.07030.05240.27350.02090.242425.2171100.257428.7926
440.00890.00660.00870.0091-0.01130.02260.05880.05890.06870.06590.0795-0.0477-0.09880.0613-0.00010.2895-0.03670.04160.1772-0.01290.185616.398394.921026.9452
450.00430.00850.01070.00600.00780.00650.06600.0949-0.0558-0.0163-0.0482-0.0788-0.00050.10070.00000.3178-0.00240.04080.22770.02660.204417.722294.038714.5917
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A9A1221chain 'A' and (resid 9 through 122 )
2A123A2472chain 'A' and (resid 123 through 247 )
3A248A3353chain 'A' and (resid 248 through 335 )
4B9B284chain 'B' and (resid 9 through 28 )
5B29B885chain 'B' and (resid 29 through 88 )
6B89B1316chain 'B' and (resid 89 through 131 )
7B132B1487chain 'B' and (resid 132 through 148 )
8B149B2128chain 'B' and (resid 149 through 212 )
9B213B2479chain 'B' and (resid 213 through 247 )
10B248B33510chain 'B' and (resid 248 through 335 )
11C9C2811chain 'C' and (resid 9 through 28 )
12C29C8812chain 'C' and (resid 29 through 88 )
13C89C13113chain 'C' and (resid 89 through 131 )
14C132C14814chain 'C' and (resid 132 through 148 )
15C149C21215chain 'C' and (resid 149 through 212 )
16C213C24716chain 'C' and (resid 213 through 247 )
17C248C29017chain 'C' and (resid 248 through 290 )
18C291C33518chain 'C' and (resid 291 through 335 )
19D9D12219chain 'D' and (resid 9 through 122 )
20D123D24720chain 'D' and (resid 123 through 247 )
21D248D33521chain 'D' and (resid 248 through 335 )
22E9E10622chain 'E' and (resid 9 through 106 )
23E107E17023chain 'E' and (resid 107 through 170 )
24E171E24724chain 'E' and (resid 171 through 247 )
25E248E33525chain 'E' and (resid 248 through 335 )
26F9F12226chain 'F' and (resid 9 through 122 )
27F123F24727chain 'F' and (resid 123 through 247 )
28F248F33528chain 'F' and (resid 248 through 335 )
29G9G2829chain 'G' and (resid 9 through 28 )
30G29G8830chain 'G' and (resid 29 through 88 )
31G89G13131chain 'G' and (resid 89 through 131 )
32G132G14832chain 'G' and (resid 132 through 148 )
33G149G17033chain 'G' and (resid 149 through 170 )
34G171G21234chain 'G' and (resid 171 through 212 )
35G213G24735chain 'G' and (resid 213 through 247 )
36G248G29036chain 'G' and (resid 248 through 290 )
37G291G33537chain 'G' and (resid 291 through 335 )
38H9H2838chain 'H' and (resid 9 through 28 )
39H29H8839chain 'H' and (resid 29 through 88 )
40H89H12240chain 'H' and (resid 89 through 122 )
41H123H15541chain 'H' and (resid 123 through 155 )
42H156H21242chain 'H' and (resid 156 through 212 )
43H213H23143chain 'H' and (resid 213 through 231 )
44H232H27444chain 'H' and (resid 232 through 274 )
45H275H33545chain 'H' and (resid 275 through 335 )

+
About Yorodumi

-
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

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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

Read more