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- PDB-5f7z: Crystal structure of Double Mutant S12T and N87T of Adenosine/Met... -

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Basic information

Entry
Database: PDB / ID: 5f7z
TitleCrystal structure of Double Mutant S12T and N87T of Adenosine/Methylthioadenosine Phosphorylase from Schistosoma mansoni in APO Form
ComponentsMethylthioadenosine phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleus / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTorini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: PLoS Negl Trop Dis / Year: 2016
Title: Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway.
Authors: Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.D.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylthioadenosine phosphorylase
B: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,13312
Polymers211,5636
Non-polymers5706
Water26,8961493
1
A: Methylthioadenosine phosphorylase
C: Methylthioadenosine phosphorylase
F: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0666
Polymers105,7823
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-66 kcal/mol
Surface area32940 Å2
MethodPISA
2
B: Methylthioadenosine phosphorylase
D: Methylthioadenosine phosphorylase
E: Methylthioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0666
Polymers105,7823
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-67 kcal/mol
Surface area32960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.701, 82.255, 150.018
Angle α, β, γ (deg.)90.000, 101.420, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTrimer confirmed by gel filtration

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Components

#1: Protein
Methylthioadenosine phosphorylase


Mass: 35260.508 Da / Num. of mol.: 6 / Fragment: Enzyme / Mutation: S12T,N87T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1493 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5 / PH range: 6.1-6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→82.26 Å / Num. obs: 178037 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.1 / Scaling rejects: 53
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.8-1.943.30.671099.9
4.76-82.263.30.05410100

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F78
Resolution: 1.8→79.103 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 8741 4.94 %Random selection
Rwork0.2107 168358 --
obs0.2119 177099 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.66 Å2 / Biso mean: 32.2947 Å2 / Biso min: 11.65 Å2
Refinement stepCycle: final / Resolution: 1.8→79.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12804 0 30 1493 14327
Biso mean--20.04 38.5 -
Num. residues----1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213074
X-RAY DIFFRACTIONf_angle_d0.53217765
X-RAY DIFFRACTIONf_chiral_restr0.0442084
X-RAY DIFFRACTIONf_plane_restr0.0042278
X-RAY DIFFRACTIONf_dihedral_angle_d10.9187817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.42042750.38855436571198
1.8205-1.84190.38443300.38275454578498
1.8419-1.86430.38712840.36185515579998
1.8643-1.88790.3912940.3665522581698
1.8879-1.91280.37262730.33955559583299
1.9128-1.9390.36292640.32145542580699
1.939-1.96670.30472620.31085643590599
1.9667-1.9960.34793270.30415537586499
1.996-2.02720.32782870.286556135900100
2.0272-2.06050.29632960.282356615957100
2.0605-2.0960.2993040.26755585862100
2.096-2.13410.29612950.263856195914100
2.1341-2.17520.31652970.255555855882100
2.1752-2.21960.27232760.235256615937100
2.2196-2.26780.24832620.2355895851100
2.2678-2.32060.24122830.223356535936100
2.3206-2.37860.26772760.214456395915100
2.3786-2.4430.23612740.211356435917100
2.443-2.51490.24162970.207556415938100
2.5149-2.5960.2392600.208256275887100
2.596-2.68880.23483000.194656335933100
2.6888-2.79650.21753210.197656135934100
2.7965-2.92380.22622840.194456475931100
2.9238-3.07790.23263420.198955885930100
3.0779-3.27080.20963140.19256565970100
3.2708-3.52330.21123080.183356645972100
3.5233-3.87780.19612800.164156775957100
3.8778-4.43890.1573050.147356775982100
4.4389-5.59240.162820.152357095991100
5.5924-79.1790.19262890.17995797608699
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)
10.7826-0.9605-1.14592.75071.59932.2696-0.44710.5685-0.63310.14120.11630.35830.5903-0.29320.32770.2765-0.03020.03590.3103-0.1020.332594.5452-18.507131.0457
21.532-0.4408-0.36691.11310.42981.9681-0.05730.1224-0.32930.0613-0.0540.09120.3269-0.03110.06430.24360.00810.03530.1896-0.0440.250296.4991-16.629239.1376
31.9241-0.069-0.29981.13010.23421.51880.06610.18280.0130.0235-0.03170.1566-0.284-0.1763-0.05010.2510.02740.02110.22-0.02690.192291.68070.55341.3439
41.328-0.98350.87351.45360.4891.8087-0.02020.0567-0.10770.1235-0.00690.00180.28610.0743-0.05370.2238-0.01210.04890.17510.00350.1749106.4098-4.722448.6441
51.9559-0.1979-0.06570.83780.26551.8120.30090.51460.3391-0.3405-0.17340.0059-0.6097-0.2333-0.06330.38970.1210.03290.32750.03080.234592.69824.53825.8349
61.3084-0.7169-0.71910.49080.47810.90540.08990.1682-0.0017-0.0182-0.12690.0866-0.2071-0.1618-0.01620.23410.0290.03460.1852-0.02620.189189.19211.337744.4199
70.07070.152-0.10320.3833-0.37240.3155-0.1079-0.4295-0.35780.16930.13680.4151-0.117-0.35250.11230.24440.09970.01150.4114-0.03210.352682.0615-2.305235.3302
86.56660.5508-0.44230.9836-0.27271.0218-0.06590.3961-0.1779-0.232-0.10410.21520.1205-0.52310.06510.28770.0216-0.02860.461-0.13650.245485.8057-8.16825.599
91.14680.13250.1450.53220.41525.2738-0.01350.123-0.0616-0.04550.0974-0.1773-0.03041.1608-0.06060.28010.05940.06340.4099-0.00160.3059114.1431-5.463638.3729
100.34630.6373-0.80552.0345-1.31111.5671-0.3328-0.4578-1.1163-0.0063-0.2877-0.42460.44860.3410.54470.3692-0.04980.10040.42450.15040.4526133.126721.469643.62
111.27250.3157-0.47271.2875-0.73241.09550.0995-0.2445-0.08910.2395-0.13440.0762-0.08520.04460.0540.2478-0.05270.03910.22350.02130.1877134.581135.87836.3265
120.1296-0.28910.46251.2203-0.19531.6939-0.1142-0.0020.09810.1719-0.1215-0.1521-0.23740.41920.10110.2726-0.1047-0.00120.37820.09220.226140.03536.575436.3594
130.2640.2974-0.74661.3662-0.24352.556-0.0043-0.3447-0.04760.3701-0.19780.0830.02980.00060.16160.3698-0.09830.06590.32180.06330.2558130.693733.359443.2422
141.64150.91010.55673.3372-0.34161.9152-0.0306-0.2539-0.15940.5662-0.11770.45760.3118-0.44440.11780.3374-0.06490.16120.30630.01190.473867.6263-7.142872.3778
151.6883-0.2123-0.37211.9667-0.40662.0056-0.0570.0825-0.30680.0669-0.00230.20060.1102-0.24020.03760.1851-0.00240.05960.16310.01210.285373.1721-0.135365.1209
161.8156-0.2184-0.83171.55260.42722.1364-0.12960.1445-0.34890.0124-0.05970.5592-0.0488-0.25090.13530.19780.01570.02780.26030.01680.316967.46525.44756.36
171.34080.3004-0.03680.50410.08311.3030.02040.12920.0055-0.00450.04990.0741-0.1531-0.0713-0.07410.22640.03110.05180.14520.0210.235678.578110.745760.8763
180.5127-0.6494-0.71120.72770.63011.6741-0.1092-0.1678-0.2075-0.44310.4899-0.7153-0.69980.2359-0.40050.29370.00260.06440.2444-0.04780.426277.155312.743169.763
194.91181.68422.35271.96421.36343.3257-0.1573-1.05350.22760.099-0.120.3524-0.4151-0.62350.23020.40040.08740.16080.39760.00080.406566.477311.446674.3296
202.0322-0.2477-0.17371.3815-0.75621.8237-0.21210.7985-0.595-0.1402-0.05990.48340.7407-0.81950.02070.4043-0.1411-0.05970.5503-0.10760.65263.6564-8.053349.1297
214.3211-3.9491-0.34224.25590.39270.52060.22360.908-0.5036-0.9301-0.3788-0.64670.4770.47340.05260.29090.06980.09520.3339-0.02670.4629162.758936.50010.5468
221.29810.2735-0.13532.2530.64521.6372-0.02160.0077-0.2124-0.0716-0.0449-0.23840.11210.19110.06040.110.00750.00360.13790.01020.1989155.41537.22386.5268
231.32540.14-0.31910.8403-0.0961.3260.0261-0.1455-0.02820.0692-0.0836-0.1387-0.04110.15060.07870.1272-0.0217-0.03450.16960.00560.1725153.846945.803915.1848
242.86010.8105-0.60941.6892-0.25741.79050.01860.0154-0.10460.055-0.0474-0.2783-0.05530.284-0.00240.1328-0.0176-0.01620.1733-0.02690.2311160.58342.60749.7633
250.66580.03911.5020.72960.81794.2854-0.0590.5674-0.0856-0.2379-0.01710.81630.7191-1.19250.00110.2632-0.0021-0.08550.602-0.10220.3627110.364947.44762.1867
260.90460.5498-0.47271.29180.37530.75-0.01391.1276-0.3568-0.3143-0.3110.78440.0722-0.87390.2340.3042-0.0394-0.05710.5629-0.19280.4415116.339334.5191-0.4953
271.7211-0.4136-0.71521.60080.51180.93640.12860.2062-0.006-0.0834-0.14610.0985-0.1158-0.2577-0.00490.16460.051-0.03740.2249-0.01560.1533122.241852.03147.9386
281.4810.0302-0.55471.7372-0.12361.6837-0.05-0.18040.04580.2296-0.1220.2239-0.0789-0.16880.05320.22360.0132-0.00820.19530.00330.183129.054749.020727.2439
292.3172-0.3281-0.23321.63280.19990.5260.0630.05260.01010.1307-0.05970.118-0.1581-0.1762-0.02520.18230.0377-0.00950.1595-0.01540.1642123.683450.938312.4785
301.941-0.6314-0.44751.60310.04750.40960.26090.3160.1849-0.2089-0.18710.1148-0.2204-0.2086-0.08330.25490.0798-0.06540.2848-0.04410.1903118.878254.38592.2147
311.69220.3512.47640.8918-0.69165.32480.1441-0.1376-0.17740.1473-0.0135-0.39690.37130.6352-0.03230.2768-0.0142-0.00480.26690.01190.2438117.87235.920672.6685
323.94260.2807-2.01895.5357-0.87842.6805-0.196-0.1394-0.19420.19860.0269-0.47150.06330.55960.19430.2420.048-0.01810.30460.04430.2436110.6888-6.531475.5707
331.5353-0.06340.14471.6168-0.22431.24420.0192-0.198-0.07710.23460.0226-0.0562-0.04920.2242-0.00840.2372-0.01920.00540.21410.02040.1746110.66062.588371.8157
341.5782-0.0855-0.27311.1708-0.00430.9740.0624-0.0126-0.02660.03220.02370.1499-0.0863-0.0321-0.07240.2315-0.01560.00430.1504-0.01150.201498.08638.541765.5949
350.706-0.0546-0.0121.61780.31130.99530.08310.02180.1280.0119-0.031-0.0218-0.22220.0577-0.03480.2537-0.03440.05010.16870.00130.2131106.717319.94459.1072
361.53820.0787-0.08291.3972-0.19980.47030.06980.0623-0.1048-0.0371-0.02810.0183-0.18130.0835-0.030.2507-0.02230.02010.1504-0.0180.1717104.449610.195762.6165
371.6151-0.05580.21312.03650.47731.12180.0466-0.28490.11060.29850.0126-0.0411-0.17780.1575-0.05040.3347-0.0423-0.02040.1680.01810.1643109.147813.553573.0714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 89 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 139 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 182 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 220 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 221 through 240 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 241 through 269 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 270 through 291 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 26 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 210 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 238 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 291 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 38 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 39 through 120 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 121 through 164 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 165 through 220 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 221 through 238 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 239 through 269 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 270 through 291 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 3 through 23 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 24 through 110 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 111 through 220 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 221 through 291 )D0
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 23 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 24 through 38 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 39 through 182 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 183 through 198 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 199 through 242 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 243 through 291 )E0
31X-RAY DIFFRACTION31chain 'F' and (resid 3 through 23 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 24 through 38 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 39 through 90 )F0
34X-RAY DIFFRACTION34chain 'F' and (resid 91 through 139 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 140 through 198 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 199 through 242 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 243 through 291 )F0

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