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- PDB-6q94: Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) ... -

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Open data


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Basic information

Entry
Database: PDB / ID: 6q94
TitleCrystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man
ComponentsGDP-mannose 4,6 dehydratase
KeywordsLYASE / GDP-mannose 4 / 6 dehydratase / fucosylation / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


GDP-fucose biosynthesis / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding / Notch signaling pathway / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
GDP-mannose 4,6-dehydratase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / GDP-mannose 4,6 dehydratase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPfeiffer, M. / Krojer, T. / Johansson, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Nidetzky, B. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Acs Catalysis / Year: 2019
Title: A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Authors: Pfeiffer, M. / Johansson, C. / Krojer, T. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.
History
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GDP-mannose 4,6 dehydratase
A: GDP-mannose 4,6 dehydratase
C: GDP-mannose 4,6 dehydratase
D: GDP-mannose 4,6 dehydratase
E: GDP-mannose 4,6 dehydratase
F: GDP-mannose 4,6 dehydratase
G: GDP-mannose 4,6 dehydratase
H: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,71428
Polymers320,6768
Non-polymers11,03820
Water724
1
B: GDP-mannose 4,6 dehydratase
A: GDP-mannose 4,6 dehydratase
hetero molecules

B: GDP-mannose 4,6 dehydratase
A: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,73312
Polymers160,3384
Non-polymers5,3958
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area20210 Å2
ΔGint-85 kcal/mol
Surface area48650 Å2
MethodPISA
2
C: GDP-mannose 4,6 dehydratase
D: GDP-mannose 4,6 dehydratase
E: GDP-mannose 4,6 dehydratase
F: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,85714
Polymers160,3384
Non-polymers5,51910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20760 Å2
ΔGint-86 kcal/mol
Surface area48960 Å2
MethodPISA
3
G: GDP-mannose 4,6 dehydratase
H: GDP-mannose 4,6 dehydratase
hetero molecules

G: GDP-mannose 4,6 dehydratase
H: GDP-mannose 4,6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,98116
Polymers160,3384
Non-polymers5,64312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_855-x+3,y,-z+1/21
Buried area22080 Å2
ΔGint-84 kcal/mol
Surface area47630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.620, 231.060, 383.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
GDP-mannose 4,6 dehydratase / GDP-D-mannose dehydratase / GMD


Mass: 40084.473 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMDS / Production host: Escherichia coli (E. coli) / References: UniProt: O60547, GDP-mannose 4,6-dehydratase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / Guanosine diphosphate mannose


Mass: 605.341 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.2M ammonium acetate, 0.1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.8→115.53 Å / Num. obs: 111281 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.87 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→115.53 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.46
RfactorNum. reflection% reflection
Rfree0.235 5446 4.9 %
Rwork0.1863 --
obs0.1887 111161 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→115.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22128 0 648 4 22780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623308
X-RAY DIFFRACTIONf_angle_d1.06631687
X-RAY DIFFRACTIONf_dihedral_angle_d18.1413902
X-RAY DIFFRACTIONf_chiral_restr0.0893521
X-RAY DIFFRACTIONf_plane_restr0.0054191
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.8230.923-0.59861.01320.74122.0356-0.0016-0.06590.3154-0.2407-0.00650.2369-0.6134-0.0514-0.01250.7778-0.00320.01290.46390.10680.63994.5505255.858-5.9538
20.3354-0.1266-0.0510.87360.5861.12820.02320.02120.0998-0.04250.1152-0.1948-0.14810.235-0.11970.6286-0.05030.02560.5250.04590.6322106.7205245.56590.262
30.812-0.296-0.18762.07661.51661.2820.0491-0.0310.1440.27430.3497-0.40860.09250.3668-0.32780.5836-0.0325-0.02840.5991-0.04420.7601114.6599253.406117.9075
43.5605-1.61240.053.60870.75563.25420.0092-0.16140.7874-0.43960.1166-0.6137-0.8780.2227-0.04190.8372-0.14160.08260.5475-0.06320.7832105.3084266.047813.8033
51.64680.18960.01810.97920.15130.79410.01140.04370.41010.02120.0237-0.0776-0.2810.0063-0.03140.6842-0.00450.03740.53510.03130.63881.0284247.643319.3092
61.28150.6347-0.31651.2473-0.35180.83140.2367-0.32790.20190.48790.3347-0.7043-0.20980.382-0.7740.7408-0.0614-0.02290.5396-0.08710.648786.5858248.894121.7311
70.76660.253-0.381.1987-0.37761.36720.0011-0.10640.14560.05950.04290.2534-0.1077-0.0779-0.0450.5884-0.00110.02390.51320.09580.642772.0475243.15127.8839
80.61440.7254-0.0661.54250.26060.17820.0249-0.08110.3249-0.1232-0.06680.3643-0.3626-0.07330.00560.79390.15360.00860.58830.14080.931964.1656262.2715-1.468
90.66890.5053-0.08410.5832-0.19550.22360.10380.02230.46060.0687-0.13660.3712-0.6355-0.5651-0.16150.76710.16590.03430.7550.10390.939759.4427247.37737.8867
105.38773.21340.71497.36550.02284.9740.5064-0.50050.80391.1718-0.34450.6489-0.609-0.2476-0.14940.82570.04680.09140.5499-0.03260.977373.105267.52739.9666
112.2793-0.945-0.5940.7262-0.41641.7407-0.1235-0.1418-0.58610.03320.1790.28020.1765-0.2746-0.0110.6668-0.19570.01160.71460.0510.641882.085279.906542.0655
120.95820.2117-0.53010.8846-0.43490.98350.0995-0.04750.15060.09380.06730.1656-0.1388-0.2154-0.14390.5973-0.09450.05620.67850.03510.623382.2757295.737348.79
131.3427-0.0224-1.43991.0234-0.72792.09880.1464-0.13770.23960.32960.24370.3422-0.333-0.3392-0.34040.7735-0.0760.16570.80450.02640.763970.61297.478762.4682
142.3778-2.20160.37439.4851-1.67123.4986-0.2959-0.5876-0.499-0.97721.20231.43930.7258-1.0698-0.89070.7833-0.23750.03181.01590.20550.725767.7208280.98961.9528
150.944-0.9102-0.01321.2415-0.75031.56530.4243-0.39250.17840.3184-0.1453-0.3215-0.81950.0363-0.02330.9976-0.37470.01820.8259-0.15960.7909114.5792319.975656.2013
160.7082-1.1338-0.12772.0473-0.44671.80570.4362-0.32090.48870.1905-0.6332-0.4325-0.06340.1550.05620.8744-0.32470.01020.7681-0.06220.8467120.4826311.303452.4684
171.1912-0.4504-0.48351.073-0.31831.09640.0945-0.26030.24910.3364-0.1286-0.0221-0.02170.2266-0.08090.6842-0.30440.0550.7227-0.0670.6204106.352305.975652.5382
180.97970.166-0.15180.5494-0.06710.78890.1491-0.24360.4810.2961-0.12280.1209-0.4732-0.0357-0.05680.8164-0.12450.16850.6364-0.0960.742894.414314.099651.6183
191.10970.2827-0.57520.9160.05421.1360.2133-0.02860.30740.4053-0.2009-0.0775-0.3593-0.058-0.00730.8136-0.18160.15370.60610.01690.9059107.801323.242840.0622
201.96020.0745-1.61251.2094-0.69572.91240.8555-0.13580.9870.7391-0.00560.3608-1.6662-0.0406-0.89011.084-0.18970.28850.6118-0.031.1813101.7169329.000740.5365
211.95420.9662-0.65971.8396-0.75310.99290.11690.41090.5716-0.02730.24440.3133-0.0717-0.6505-0.31570.6681-0.08570.09180.73250.21820.9915105.9941325.697917.4157
221.56160.3932-0.84660.2833-0.320.65850.4435-0.48170.65590.2845-0.15010.2497-0.9758-0.304-0.34891.1734-0.05530.24580.7797-0.01421.071796.7615326.446844.4261
234.84450.9196-0.47732.2363-0.24734.45840.7402-0.26541.58320.7545-0.3327-0.3502-1.26450.5012-0.35971.0739-0.30080.15920.7546-0.04211.0466118.3518329.143134.1694
242.2861-0.42670.93482.0047-0.67571.89650.1429-0.461-0.29490.40690.14570.40130.1065-0.1461-0.23050.7617-0.1746-0.00830.88080.05260.538495.7401277.151568.1071
251.1110.47070.071.0812-0.32191.36720.1068-0.2563-0.2580.2219-0.1526-0.14340.28870.16370.05270.6704-0.0867-0.05370.66190.07760.6114104.5743268.020653.4098
261.65460.81670.5981.5074-0.16721.77170.1112-0.5855-0.44350.1067-0.05190.04080.819-0.0263-0.12630.8256-0.0479-0.05870.62850.16390.6709101.2087258.791156.9833
272.7072-0.7895-0.25191.82440.61012.10880.0810.31450.5119-0.0013-0.0698-0.6936-0.24490.4332-0.05290.6377-0.11520.04120.70830.12570.7187120.6884300.825827.8743
281.67340.6789-0.62522.1986-0.55411.17480.2689-0.30510.08450.287-0.381-0.6996-0.01790.45660.10050.5268-0.1122-0.08270.72380.11060.771129.1517291.011842.6834
291.53771.90380.74842.40450.96881.6068-0.00850.0320.1187-0.0733-0.0795-0.70430.02270.72660.11250.6586-0.0045-0.06321.02510.23321.1186138.6335293.986439.3297
302.8562-0.61310.22411.2291-0.36851.86130.33080.4288-0.1197-0.24290.05910.22280.1005-0.5183-0.42010.7825-0.0120.00340.9605-0.01450.5721135.8255266.713476.7142
311.56320.2370.44961.08560.39522.29860.14530.0737-0.053-0.0368-0.06370.2034-0.1679-0.0216-0.08950.6440.03180.08370.7873-0.00020.4567144.2838272.651885.5266
321.77880.0116-0.01360.67470.45252.04730.2576-0.08010.1792-0.0258-0.07150.1214-0.3941-0.7111-0.02160.68660.11780.06841.05220.06160.6393125.0996278.357989.9941
331.8893-0.20380.60560.29130.16331.5916-0.0809-0.18520.2645-0.02940.02140.2046-0.2329-0.87590.01980.82840.18470.06781.1282-0.06020.6297121.5072283.749397.5732
341.55350.6408-0.41481.748-0.05190.1758-0.4123-0.34270.2243-0.18570.2009-0.0931-0.237-0.13790.13850.95750.16990.06570.88390.09390.6827136.0368288.635287.5686
355.42683.24890.09625.81510.07193.203-0.32680.8774-0.3084-1.0870.278-0.0127-0.2043-1.05040.05910.87480.15090.09131.22050.06440.659115.9695274.26986.3432
361.6815-0.08240.95871.56680.8261.64930.5107-0.1231-0.6033-0.037-0.0410.26160.7526-0.4364-0.06491.0656-0.2353-0.08671.09680.24230.8307126.9923247.3741103.6807
371.13030.30450.01191.15710.10010.8569-0.0037-0.185-0.3574-0.1905-0.09710.26530.2401-0.6015-0.04730.8648-0.1872-0.04351.15390.17850.7143128.7098256.7695100.6675
381.0225-0.01440.47381.5087-0.16642.29880.2487-0.0975-0.40040.06240.12230.09380.1856-0.0409-0.42140.8893-0.0881-0.12670.9050.08030.7462142.2672251.2833100.3515
391.90460.1142-0.48721.8076-0.44591.13630.3396-0.2603-0.9884-0.0051-0.08080.38040.6951-0.3167-0.18481.2564-0.1588-0.37140.78820.14051.1401145.2501237.270999.4049
401.4842-0.03140.64371.6955-0.9151.80960.3426-0.0522-0.6234-0.2148-0.05110.07310.6948-0.6079-0.35491.1602-0.104-0.35230.87890.00121.1715129.0978241.716283.5848
411.45580.0741-0.51741.1263-0.23820.23530.47640.148-0.9235-0.0188-0.04870.01350.58050.1584-0.33621.1888-0.1432-0.42890.88470.00231.2027129.1081234.615182.1355
420.36-0.36940.18670.6072-0.29860.13510.2985-0.1136-0.9130.46390.0289-0.13780.5427-0.1595-0.35281.3589-0.1992-0.37680.91080.09071.4111134.1053229.6493.66
433.8585-0.17510.16491.516-0.10353.1026-0.2309-0.1131-0.4739-0.22630.1488-0.1404-0.1927-0.78840.18911.1121-0.281-0.40831.18440.09661.1663117.5157243.201582.1117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 23 through 89 )
2X-RAY DIFFRACTION2chain 'B' and (resid 90 through 280 )
3X-RAY DIFFRACTION3chain 'B' and (resid 281 through 350 )
4X-RAY DIFFRACTION4chain 'B' and (resid 351 through 372 )
5X-RAY DIFFRACTION5chain 'A' and (resid 23 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 264 )
8X-RAY DIFFRACTION8chain 'A' and (resid 265 through 323 )
9X-RAY DIFFRACTION9chain 'A' and (resid 324 through 350 )
10X-RAY DIFFRACTION10chain 'A' and (resid 351 through 372 )
11X-RAY DIFFRACTION11chain 'C' and (resid 23 through 89 )
12X-RAY DIFFRACTION12chain 'C' and (resid 90 through 264 )
13X-RAY DIFFRACTION13chain 'C' and (resid 265 through 350 )
14X-RAY DIFFRACTION14chain 'C' and (resid 351 through 372 )
15X-RAY DIFFRACTION15chain 'D' and (resid 23 through 46 )
16X-RAY DIFFRACTION16chain 'D' and (resid 47 through 89 )
17X-RAY DIFFRACTION17chain 'D' and (resid 90 through 141 )
18X-RAY DIFFRACTION18chain 'D' and (resid 142 through 197 )
19X-RAY DIFFRACTION19chain 'D' and (resid 198 through 264 )
20X-RAY DIFFRACTION20chain 'D' and (resid 265 through 292 )
21X-RAY DIFFRACTION21chain 'D' and (resid 293 through 323 )
22X-RAY DIFFRACTION22chain 'D' and (resid 324 through 350 )
23X-RAY DIFFRACTION23chain 'D' and (resid 351 through 372 )
24X-RAY DIFFRACTION24chain 'E' and (resid 23 through 89 )
25X-RAY DIFFRACTION25chain 'E' and (resid 90 through 323 )
26X-RAY DIFFRACTION26chain 'E' and (resid 324 through 372 )
27X-RAY DIFFRACTION27chain 'F' and (resid 23 through 89 )
28X-RAY DIFFRACTION28chain 'F' and (resid 90 through 323 )
29X-RAY DIFFRACTION29chain 'F' and (resid 324 through 372 )
30X-RAY DIFFRACTION30chain 'G' and (resid 23 through 65 )
31X-RAY DIFFRACTION31chain 'G' and (resid 66 through 218 )
32X-RAY DIFFRACTION32chain 'G' and (resid 219 through 264 )
33X-RAY DIFFRACTION33chain 'G' and (resid 265 through 323 )
34X-RAY DIFFRACTION34chain 'G' and (resid 324 through 350 )
35X-RAY DIFFRACTION35chain 'G' and (resid 351 through 372 )
36X-RAY DIFFRACTION36chain 'H' and (resid 23 through 45 )
37X-RAY DIFFRACTION37chain 'H' and (resid 46 through 89 )
38X-RAY DIFFRACTION38chain 'H' and (resid 90 through 141 )
39X-RAY DIFFRACTION39chain 'H' and (resid 142 through 197 )
40X-RAY DIFFRACTION40chain 'H' and (resid 198 through 245 )
41X-RAY DIFFRACTION41chain 'H' and (resid 246 through 323 )
42X-RAY DIFFRACTION42chain 'H' and (resid 324 through 350 )
43X-RAY DIFFRACTION43chain 'H' and (resid 351 through 372 )

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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.
  • 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

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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

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