[English] 日本語
Yorodumi
- PDB-4l5c: Methylthioadenosine phosphorylase from Schistosoma mansoni in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l5c
TitleMethylthioadenosine phosphorylase from Schistosoma mansoni in complex with adenine in space group P212121
ComponentsS-methyl-5'-thioadenosine phosphorylase
KeywordsTRANSFERASE / phsophorylase / Nucleoside phosphorylase / Enzyme
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
ADENINE / S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.075 Å
AuthorsTorini, J.R. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.M.
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
DepositionJun 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-methyl-5'-thioadenosine phosphorylase
B: S-methyl-5'-thioadenosine phosphorylase
C: S-methyl-5'-thioadenosine phosphorylase
D: S-methyl-5'-thioadenosine phosphorylase
E: S-methyl-5'-thioadenosine phosphorylase
F: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,92018
Polymers211,5576
Non-polymers1,36312
Water23,2391290
1
A: S-methyl-5'-thioadenosine phosphorylase
B: S-methyl-5'-thioadenosine phosphorylase
C: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4609
Polymers105,7783
Non-polymers6826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9350 Å2
ΔGint-37 kcal/mol
Surface area30780 Å2
MethodPISA
2
D: S-methyl-5'-thioadenosine phosphorylase
E: S-methyl-5'-thioadenosine phosphorylase
F: S-methyl-5'-thioadenosine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4609
Polymers105,7783
Non-polymers6826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-38 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.580, 135.710, 145.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase


Mass: 35259.480 Da / Num. of mol.: 6 / Fragment: SmMTAP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Strain: BH / Gene: SmMTAP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1290 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2011 / Details: DCM
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.075→59.219 Å / Num. all: 122620 / Num. obs: 122620 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rsym value: 0.119 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.075-2.137.30.6951.16593489870.69599.6
2.13-2.197.30.6141.26368686900.61499.8
2.19-2.257.30.491.56218585070.4999.7
2.25-2.327.30.4091.86030782670.40999.7
2.32-2.47.30.3332.25844380390.33399.8
2.4-2.487.30.2852.65646777500.28599.9
2.48-2.577.30.2435471175320.24100
2.57-2.687.30.1943.75224572010.19499.9
2.68-2.87.20.1634.35048869930.163100
2.8-2.937.20.13754793166420.13799.9
2.93-3.097.20.1175.74521263040.117100
3.09-3.287.10.16.54290160160.199.9
3.28-3.517.10.0857.13979056360.085100
3.51-3.7970.0767.53696653160.07699.9
3.79-4.156.90.06883353848580.068100
4.15-4.646.90.0638.53042944240.06399.9
4.64-5.366.80.0628.62671339320.06299.9
5.36-6.5670.05810.22365833560.058100
6.56-9.287.10.04911.71874426420.04999.9
9.28-59.2196.60.04113.41001615280.04199.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LJI
Resolution: 2.075→59.219 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.786 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 6153 5.02 %Random
Rwork0.1911 ---
all0.1926 122620 --
obs0.1926 122450 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.83 Å2 / Biso mean: 26.6766 Å2 / Biso min: 7.64 Å2
Refinement stepCycle: LAST / Resolution: 2.075→59.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13260 0 96 1290 14646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313625
X-RAY DIFFRACTIONf_angle_d0.68318462
X-RAY DIFFRACTIONf_chiral_restr0.0432121
X-RAY DIFFRACTIONf_plane_restr0.0032357
X-RAY DIFFRACTIONf_dihedral_angle_d11.6744932
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 (%)
2.075-2.09860.29442150.254538494064100
2.0986-2.12330.32072070.25137693976100
2.1233-2.14920.28942120.251938664078100
2.1492-2.17640.28912190.245138024021100
2.1764-2.2050.28992100.237938154025100
2.205-2.23520.25591920.214438564048100
2.2352-2.26720.25891800.212538704050100
2.2672-2.3010.24462230.209738274050100
2.301-2.3370.25861970.219238384035100
2.337-2.37530.26232220.218438054027100
2.3753-2.41620.26312170.20838294046100
2.4162-2.46020.26281990.213738664065100
2.4602-2.50750.25221890.208238604049100
2.5075-2.55870.24872020.20638564058100
2.5587-2.61430.24842020.212738974099100
2.6143-2.67510.24051900.207138304020100
2.6751-2.7420.23051850.1938714056100
2.742-2.81620.25271980.199938714069100
2.8162-2.8990.24452370.198338654102100
2.899-2.99260.22391870.201938764063100
2.9926-3.09960.22342060.20238984104100
3.0996-3.22370.23182010.197738914092100
3.2237-3.37040.22911740.189939074081100
3.3704-3.5480.20712030.189339344137100
3.548-3.77030.20062110.173639004111100
3.7703-4.06130.19872030.16539114114100
4.0613-4.46990.1782090.144639364145100
4.4699-5.11640.14632320.145339214153100
5.1164-6.44490.19912160.171239964212100
6.4449-59.24320.17792150.17844085430098
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)
10.73380.0360.04160.6769-0.15560.4813-0.07080.0828-0.09770.0458-0.00230.25560.0723-0.16110.06890.1284-0.01570.01680.1465-0.00910.2094-12.92334.6359-36.9632
20.57510.49520.10280.84840.1620.6697-0.01590.0171-0.03220.11980.0418-0.07710.09930.0875-0.02950.11790.0245-0.00840.10990.0070.10156.167135.3711-33.7744
30.78420.19980.43521.6138-0.0910.4462-0.13660.0049-0.08760.00120.0832-0.0950.16970.14460.00970.113-0.008-0.02170.0689-0.01260.11694.709435.4658-39.2919
40.50630.28590.01141.25820.08230.30680.0101-0.0669-0.0840.1801-0.00360.16050.1742-0.02510.030.14650.0090.01890.13810.0230.1515-4.771330.2363-30.527
50.83560.3593-0.29580.1927-0.07411.4956-0.22520.25750.392-0.34550.06580.2107-0.43360.0178-0.13080.3631-0.0985-0.09470.22380.09930.1936.697867.7455-65.0859
60.6579-0.005-0.02570.36960.35630.8412-0.17520.13340.1806-0.17040.06820.1148-0.1269-0.01290.04010.1808-0.0421-0.07370.15390.04720.13576.358363.4329-56.1617
71.00830.51970.08931.21990.14470.6235-0.11080.0816-0.0173-0.14150.08020.003-0.07860.0380.00320.13670.00080.00420.13440.00740.074910.694753.0163-50.2712
80.53340.2144-0.08720.4682-0.05410.5962-0.10370.08020.0561-0.16370.0911-0.12270.08930.08530.01820.1595-0.01930.02190.1812-0.00160.110424.60756.8644-51.0448
90.7677-0.2976-0.32230.9425-0.37210.6777-0.03960.0178-0.0371-0.0770.1084-0.2008-0.08240.10960.01220.1025-0.03660.02490.12180.02450.086218.499860.6396-49.0121
100.4077-0.247-0.22680.1737-0.11310.9478-0.16650.24460.1899-0.36210.13930.0351-0.12210.0816-0.03340.2674-0.09670.00440.2380.05040.036414.57357.8033-62.0173
110.3664-0.1910.48062.2230.21381.1298-0.019-0.23440.08780.53010.05450.29590.0936-0.32060.02520.37670.0404-0.03580.2357-0.07680.27543.042272.5248-11.3938
120.6185-0.1329-1.30270.35860.47172.8718-0.06450.00040.10030.03570.08620.2033-0.0778-0.41350.03870.12520.0468-0.01640.1734-0.01580.1775-6.149175.0314-22.7861
130.4742-0.06110.09740.87210.14480.1951-0.0523-0.17240.0970.21170.06410.0942-0.0919-0.06740.02890.18540.01750.01440.1413-0.03550.14182.225970.8772-19.3597
140.6654-0.02190.09641.3233-0.48421.14150.0063-0.00540.0506-0.01950.01810.05530.05180.084-0.02340.10840.0034-0.0230.1268-0.03080.095811.356263.6704-28.86
150.39320.2472-0.05790.68930.33390.690.013-0.04570.05450.20390.0946-0.20350.06690.2174-0.04390.15360.0241-0.07360.1881-0.04720.155818.48857.756-17.6654
161.0362-0.0514-0.04620.34040.46390.71880.0324-0.1414-0.01330.1605-0.0812-0.21010.1470.0573-0.01970.1489-0.0091-0.01970.1199-0.02340.079411.339857.6105-19.7314
170.6807-0.05340.3180.80020.47130.7127-0.0197-0.16430.16860.16360.01130.0177-0.1440.13740.00870.1846-0.0066-0.01940.1608-0.07020.183912.35471.5539-18.6425
180.85210.0346-0.04950.65330.20550.3812-0.10410.04970.1459-0.01340.067-0.2842-0.09590.11340.03080.1297-0.0096-0.00470.17110.00490.280564.104835.6351-36.9257
190.5680.6658-0.16970.9908-0.17160.68690.01670.01920.11740.22120.10530.1539-0.0612-0.0449-0.06210.16850.03480.04540.13980.00080.225446.431536.8833-31.2262
200.86210.3785-0.22531.4555-0.0030.4818-0.03760.0820.12750.10540.09410.0906-0.0270.0344-0.06080.12930.02420.020.11810.00480.209749.242535.5375-35.7576
211.0282-0.37620.03110.4416-0.19880.5688-0.0949-0.37770.05030.5983-0.0554-0.2659-0.23790.22460.0390.48260.01830.01350.3290.14360.368948.873-3.8377-12.2573
220.338-0.19020.29070.29440.03881.367-0.0351-0.1726-0.25350.23350.0094-0.02080.12930.11360.00850.23940.06050.02820.23090.08540.238952.4241-6.2253-17.9898
233.68911.20610.00692.52231.55231.1272-0.1485-0.41350.17640.64240.194-0.3840.0176-0.0599-0.07820.31680.064-0.02040.21010.00850.261354.6298.4264-21.0641
240.82780.3539-0.04810.6480.17140.81580.102-0.1423-0.12540.1411-0.05680.0264-0.062-0.0986-0.03370.19420.01790.0520.16810.0430.17941.73245.5595-23.8857
250.5023-0.2901-0.28740.730.1511.80060.0266-0.005-0.23470.068-0.0980.0299-0.0743-0.1753-0.05880.1558-0.01110.0510.16690.03240.260936.778-1.2339-26.5226
261.32621.2056-0.2691.65250.19612.2436-0.1112-0.22580.22310.34850.07990.6231-0.1917-0.5956-0.13390.40080.0250.21380.37780.00890.335825.40410.8958-10.1961
270.3750.21330.12620.5264-0.02710.32590.0454-0.02480.05280.11790.01420.0881-0.0534-0.0069-0.06950.18220.03080.07090.16310.01790.199939.920613.1259-24.8626
284.2798-1.7071-0.1041.7946-1.4491.99490.0201-0.32510.51870.5005-0.03890.0513-0.46360.05850.00150.43880.00560.10160.23-0.0760.225839.831925.3104-14.54
290.6189-0.0815-0.33180.6553-0.37150.65330.0304-0.1973-0.24050.2467-0.0012-0.0690.0504-0.16130.01490.2768-0.01720.02650.2390.09670.225638.8519-1.6716-18.8834
300.79070.4310.64170.38450.0371.3726-0.1680.5684-0.4923-0.2740.1272-0.22040.5292-0.180.64870.3608-0.17680.19630.6279-0.34090.342444.27862.8114-65.0334
310.59080.0448-0.00550.0362-0.05360.4215-0.22480.5165-0.3464-0.00160.1716-0.09130.1578-0.01540.12820.1962-0.09980.13920.3322-0.09880.233144.67327.0874-56.2948
321.26610.699-0.18711.0201-0.08840.4696-0.18930.21170.0019-0.12840.1762-0.0159-0.0224-0.017-0.02040.136-0.03140.0120.2322-0.00190.169640.554417.3784-50.2473
330.79190.39850.24540.58140.18670.3371-0.23560.1904-0.0467-0.01770.18280.129-0.09110.0353-0.01250.1138-0.04390.020.20270.01270.177126.4413.4949-50.9256
340.8702-0.28280.3480.92950.44640.6896-0.09670.2003-0.02970.05310.1810.15980.0846-0.05540.00710.1311-0.03440.01540.1821-0.00550.204332.61239.7268-48.9965
350.5776-0.12840.15130.11440.23690.7418-0.2980.5678-0.1609-0.23670.3368-0.0632-0.0381-0.07560.07020.2193-0.13890.01580.4246-0.01440.156936.370212.7244-61.9733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 210 )
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 242 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 291 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 90 )
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 210 )
9X-RAY DIFFRACTION9chain 'B' and (resid 211 through 242 )
10X-RAY DIFFRACTION10chain 'B' and (resid 243 through 291 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 23 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 38 )
13X-RAY DIFFRACTION13chain 'C' and (resid 39 through 90 )
14X-RAY DIFFRACTION14chain 'C' and (resid 91 through 139 )
15X-RAY DIFFRACTION15chain 'C' and (resid 140 through 210 )
16X-RAY DIFFRACTION16chain 'C' and (resid 211 through 242 )
17X-RAY DIFFRACTION17chain 'C' and (resid 243 through 292 )
18X-RAY DIFFRACTION18chain 'D' and (resid 3 through 90 )
19X-RAY DIFFRACTION19chain 'D' and (resid 91 through 182 )
20X-RAY DIFFRACTION20chain 'D' and (resid 183 through 291 )
21X-RAY DIFFRACTION21chain 'E' and (resid 3 through 26 )
22X-RAY DIFFRACTION22chain 'E' and (resid 27 through 53 )
23X-RAY DIFFRACTION23chain 'E' and (resid 54 through 67 )
24X-RAY DIFFRACTION24chain 'E' and (resid 68 through 120 )
25X-RAY DIFFRACTION25chain 'E' and (resid 121 through 152 )
26X-RAY DIFFRACTION26chain 'E' and (resid 153 through 177 )
27X-RAY DIFFRACTION27chain 'E' and (resid 178 through 227 )
28X-RAY DIFFRACTION28chain 'E' and (resid 228 through 242 )
29X-RAY DIFFRACTION29chain 'E' and (resid 243 through 292 )
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 53 )
31X-RAY DIFFRACTION31chain 'F' and (resid 54 through 90 )
32X-RAY DIFFRACTION32chain 'F' and (resid 91 through 139 )
33X-RAY DIFFRACTION33chain 'F' and (resid 140 through 210 )
34X-RAY DIFFRACTION34chain 'F' and (resid 211 through 242 )
35X-RAY DIFFRACTION35chain 'F' and (resid 243 through 291 )

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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

Read more