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- PDB-4qh6: Crystal structure of cruzain with nitrile inhibitor N-(2-AMINOETH... -

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Basic information

Entry
Database: PDB / ID: 4qh6
TitleCrystal structure of cruzain with nitrile inhibitor N-(2-AMINOETHYL)-NALPHA-BENZOYL-L-PHENYLALANINAMIDE
ComponentsCruzipain
KeywordsHydrolase/Hydrolase inhibitor / Thiol protease / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


cruzipain / cysteine-type endopeptidase activity / proteolysis
Similarity search - Function
Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Domain of unknown function DUF3586 / Protein of unknown function (DUF3586) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-33L / Cruzipain
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsFernandes, W.B. / Montanari, C.A. / McKerrow, J.H.
CitationJournal: Plos Negl Trop Dis / Year: 2015
Title: Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors.
Authors: Avelar, L.A. / Camilo, C.D. / de Albuquerque, S. / Fernandes, W.B. / Goncalez, C. / Kenny, P.W. / Leitao, A. / McKerrow, J.H. / Montanari, C.A. / Orozco, E.V. / Ribeiro, J.F. / Rocha, J.R. / ...Authors: Avelar, L.A. / Camilo, C.D. / de Albuquerque, S. / Fernandes, W.B. / Goncalez, C. / Kenny, P.W. / Leitao, A. / McKerrow, J.H. / Montanari, C.A. / Orozco, E.V. / Ribeiro, J.F. / Rocha, J.R. / Rosini, F. / Saidel, M.E.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Sep 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cruzipain
B: Cruzipain
C: Cruzipain
D: Cruzipain
E: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8876
Polymers113,5765
Non-polymers3111
Water0
1
A: Cruzipain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0272
Polymers22,7151
Non-polymers3111
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cruzipain


Theoretical massNumber of molelcules
Total (without water)22,7151
Polymers22,7151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.790, 137.790, 166.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Cruzipain / / Cruzaine / Major cysteine proteinase


Mass: 22715.133 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Cruzipain, GenBank M84342.1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P25779, cruzipain
#2: Chemical ChemComp-33L / N-(2-aminoethyl)-Nalpha-benzoyl-L-phenylalaninamide / Nalpha-benzoyl-N-[(2Z)-2-iminoethyl]-L-phenylalaninamide, bound form


Mass: 311.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H21N3O2

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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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 1.2M K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 3.13→34.731 Å / Num. obs: 28790 / % possible obs: 99.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.128

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
ELVESrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KKU
Resolution: 3.13→34.731 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1440 5.01 %RAMDOM
Rwork0.2042 ---
obs0.2062 28746 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.13→34.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7960 0 23 0 7983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058195
X-RAY DIFFRACTIONf_angle_d0.86611190
X-RAY DIFFRACTIONf_dihedral_angle_d11.2942744
X-RAY DIFFRACTIONf_chiral_restr0.0371236
X-RAY DIFFRACTIONf_plane_restr0.0041455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1299-3.24170.37581400.33992655X-RAY DIFFRACTION99
3.2417-3.37140.34781420.30172684X-RAY DIFFRACTION100
3.3714-3.52470.29671410.25752665X-RAY DIFFRACTION99
3.5247-3.71030.3161420.23662694X-RAY DIFFRACTION99
3.7103-3.94250.2541430.21842715X-RAY DIFFRACTION99
3.9425-4.24640.24911420.1992693X-RAY DIFFRACTION99
4.2464-4.67280.22181440.16632729X-RAY DIFFRACTION100
4.6728-5.34690.21291440.17112734X-RAY DIFFRACTION100
5.3469-6.72850.24641470.19432800X-RAY DIFFRACTION100
6.7285-34.73280.19011550.17822937X-RAY DIFFRACTION100
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)
11.53590.147-0.3121.0779-0.44922.26560.10730.0299-0.31830.08630.064-0.6265-0.23360.3727-0.09560.3298-0.0630.02320.50230.0060.400811.985116.28718.3417
21.23640.1243-0.14942.39140.25921.38510.08180.0471-0.0497-0.14670.0029-0.1052-0.23010.0981-0.00650.3272-0.02710.10950.21540.04750.4195.414722.709512.2033
31.6467-1.4961-0.40781.8420.31641.73620.3846-0.09050.84970.32070.1473-0.0431-1.2128-0.4019-0.0571.07960.30090.15950.55640.07390.4862-1.535631.526718.4728
42.63731.90081.11912.59751.03912.86430.13510.2587-0.3537-0.32850.1434-0.6291-0.74140.6546-0.09480.6684-0.12560.21930.4397-0.00570.58797.482630.77778.4703
50.2797-0.2576-0.06910.65140.2420.07730.1755-0.24480.27160.69230.3980.3087-0.77740.06980.1190.52610.0250.09490.26410.00370.41290.39527.204613.4601
61.2491-0.00880.20281.37220.00881.39670.19680.0424-0.05160.23380.0428-0.3148-0.51020.3179-0.1280.3887-0.05420.06850.2189-0.02460.33689.658315.377929.3342
70.7748-0.18580.69241.9454-0.0970.6670.19820.16080.1086-0.4630.1389-0.2605-0.4340.6668-0.10040.3944-0.19540.12640.5767-0.04690.392216.65417.670526.4958
81.6206-0.81822.07110.8269-0.52086.76920.0252-0.1061-0.03290.51260.35620.1837-0.0934-0.38440.06110.4925-0.1550.03420.16060.03540.38671.064818.460926.7643
92.1214-0.53450.54272.71980.30412.12620.34810.0576-0.2043-0.3894-0.25590.80620.4314-0.79740.27050.5295-0.00810.00460.6335-0.14980.6515-15.442724.333-11.3644
101.86870.23360.041.5629-0.32562.32440.0281-0.2588-0.36410.0865-0.13040.77670.2114-0.42030.04080.30240.03270.05610.2707-0.04680.427-13.326135.0015-9.5762
111.9699-0.421-1.26962.48160.07830.8254-0.21470.30210.18890.1277-0.2516-0.102-0.14110.46610.13570.3977-0.00460.05910.45920.04780.5877-1.6738.7401-13.2364
121.0237-0.43460.2591.08760.01842.32280.051-0.1454-0.1423-0.4467-0.43670.2138-0.2424-0.74270.15890.54570.20940.07460.4966-0.04190.4485-13.4344.3535-16.1582
131.5038-1.26221.05491.8483-0.07341.4006-0.3816-0.3544-0.12520.14990.1740.04810.033-0.42650.03030.5106-0.00350.15190.29840.13470.4696-4.516726.3441-1.922
140.65120.32930.4780.85540.34692.12010.123-0.0406-0.2526-0.00850.04530.1790.7751-0.85090.0260.35080.04880.03350.3302-0.03850.5531-7.076216.8273-15.5362
150.74310.4661-1.14711.12610.12412.67890.31040.6259-0.4565-0.2056-0.41720.25480.7167-0.64030.02450.41050.07730.00270.4494-0.06840.6293-11.060217.8881-17.76
162.9309-1.86310.55765.98010.13280.49070.1445-0.22320.30530.08650.2438-0.3757-0.4333-0.0159-0.26420.5080.00440.12440.50550.13220.3988-2.31526.9483-5.9821
170.9240.6668-0.0780.74370.0151.3248-0.0708-0.2119-0.21310.23110.12440.4680.166-0.93440.01140.3772-0.0877-0.04230.3980.09040.5172-18.9896-5.289937.0579
181.64080.2367-0.03440.39290.54781.4291-0.14290.43790.2786-0.0217-0.0563-0.2372-0.3036-0.9408-0.23010.11490.2664-0.07320.79520.10970.3292-21.45064.367625.5355
191.1438-0.15960.76442.615-1.49981.953-0.25620.84580.28670.43950.0685-0.224-0.6085-0.5139-0.09840.18030.10090.08890.54080.00740.3659-16.06269.104825.4073
200.85080.92310.55151.99-0.44751.55850.1930.5592-0.3844-0.77940.35870.481-0.3122-0.6441-0.15440.69480.0033-0.14621.16370.05070.5668-18.88634.344813.2791
213.6456-0.60290.87451.26010.16180.2887-0.10510.05160.79090.11030.29960.0781-0.4563-0.42440.120.28710.42350.0280.90590.17640.4664-17.276413.67322.755
222.02080.82940.1830.9008-0.7981.4324-0.08810.6260.1025-1.05420.29740.04990.1692-0.59990.15850.49980.1896-0.09080.42780.15470.2795-15.99729.834219.2158
232.31860.98770.25181.5244-0.85951.1148-0.22080.8979-0.4381-0.61460.51880.05350.8883-0.758-0.8540.3167-0.1767-0.15250.81360.0250.3986-25.4704-9.45226.3537
240.0771-0.0478-0.07410.0630.04490.0917-0.14210.19720.0589-0.0987-0.10220.2231-0.0657-0.2595-0.3880.5464-0.3728-0.34481.28030.16160.622-36.0963-10.292823.2123
250.482-0.11560.06011.31071.21751.5227-0.41020.4023-0.28480.23610.1535-0.5740.3019-0.63070.13330.2864-0.10570.02560.7247-0.02130.5214-26.1786-10.459132.5231
261.55310.5578-0.23840.4692-0.41480.97630.05880.57670.0878-0.01040.13110.26420.025-1.3174-0.02630.3827-0.0367-0.0840.9528-0.01760.4457-27.9705-5.516727.9802
270.58190.2488-0.30430.8064-0.0541.10820.3007-0.41860.33430.0523-0.3161-0.2028-0.1048-0.24580.00890.55260.1340.17840.5232-0.06810.4632-13.154662.6144.2044
282.33020.55790.11181.423-0.83841.3616-0.14350.22750.1168-0.6317-0.12060.86810.2904-0.54130.11340.7940.38380.11180.68460.02350.757-20.949864.7067-8.7065
290.4699-0.3669-0.04791.70220.06310.66410.023-0.40450.3821-0.21960.1659-0.0285-0.2371-0.31411.01560.6050.70630.31540.2603-0.33810.4663-13.080670.2642-4.9998
301.43030.68060.51082.16050.15221.890.0806-0.0478-0.05790.57810.20630.1334-0.382-1.1918-0.06650.69440.0332-0.02780.7153-0.06370.4696-17.726645.50242.5238
310.5013-0.1652-0.25850.12340.30270.69950.056-0.54210.00050.41530.42730.3342-0.4117-0.57440.65230.48670.59990.42310.9577-0.23160.2446-27.145459.00429.9213
320.04470.12620.03720.39810.11150.04530.6996-0.04550.39460.5835-0.59840.7195-0.1967-0.7575-0.01970.69720.10160.22311.7316-0.04190.9093-32.885655.062110.3273
332.10660.37860.93361.6889-0.47180.9953-0.1884-0.6064-0.01130.8385-0.58110.80130.2927-0.74980.44550.68560.10810.20770.7813-0.10440.4504-21.805655.450513.4024
341.20771.04680.04271.4439-0.53650.6258-0.0786-0.32440.13160.3115-0.0590.4744-0.0777-0.57421.21720.40370.51650.1840.4616-0.36710.4056-22.163552.46590.4539
350.61120.63520.68111.2547-0.02172.32440.15830.3721-0.0747-0.63010.5439-0.61330.06381.26-0.24790.6196-0.42780.12691.2785-0.47680.84131.149561.710119.6985
360.78880.68031.18222.81260.96061.78830.11030.76940.0432-0.21710.9062-1.9692-0.43691.7102-0.02980.6518-0.45330.2032.2276-0.65181.059313.897865.990520.5675
371.5837-1.3237-0.5261.62411.07772.06210.0568-0.0191-0.06620.18310.549-0.6710.27141.4053-0.21320.5062-0.1622-0.0511.103-0.35320.63634.147559.556424.938
380.92880.0859-0.06941.6047-0.32380.8133-0.33610.3673-0.0063-0.26361.0649-0.50890.37481.1288-0.35640.91910.1676-0.17070.8572-0.35830.71950.43854.916227.5134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 121 )
6X-RAY DIFFRACTION6chain 'A' and (resid 122 through 181 )
7X-RAY DIFFRACTION7chain 'A' and (resid 182 through 201 )
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 215 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 24 )
10X-RAY DIFFRACTION10chain 'B' and (resid 25 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 77 )
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 107 )
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 132 )
14X-RAY DIFFRACTION14chain 'B' and (resid 133 through 181 )
15X-RAY DIFFRACTION15chain 'B' and (resid 182 through 204 )
16X-RAY DIFFRACTION16chain 'B' and (resid 205 through 215 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 16 )
18X-RAY DIFFRACTION18chain 'C' and (resid 17 through 40 )
19X-RAY DIFFRACTION19chain 'C' and (resid 41 through 56 )
20X-RAY DIFFRACTION20chain 'C' and (resid 57 through 78 )
21X-RAY DIFFRACTION21chain 'C' and (resid 79 through 94 )
22X-RAY DIFFRACTION22chain 'C' and (resid 95 through 118 )
23X-RAY DIFFRACTION23chain 'C' and (resid 119 through 149 )
24X-RAY DIFFRACTION24chain 'C' and (resid 150 through 161 )
25X-RAY DIFFRACTION25chain 'C' and (resid 162 through 181 )
26X-RAY DIFFRACTION26chain 'C' and (resid 182 through 215 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 56 )
28X-RAY DIFFRACTION28chain 'D' and (resid 57 through 77 )
29X-RAY DIFFRACTION29chain 'D' and (resid 78 through 118 )
30X-RAY DIFFRACTION30chain 'D' and (resid 119 through 132 )
31X-RAY DIFFRACTION31chain 'D' and (resid 133 through 148 )
32X-RAY DIFFRACTION32chain 'D' and (resid 149 through 161 )
33X-RAY DIFFRACTION33chain 'D' and (resid 162 through 201 )
34X-RAY DIFFRACTION34chain 'D' and (resid 202 through 215 )
35X-RAY DIFFRACTION35chain 'E' and (resid 1 through 42 )
36X-RAY DIFFRACTION36chain 'E' and (resid 43 through 78 )
37X-RAY DIFFRACTION37chain 'E' and (resid 79 through 181 )
38X-RAY DIFFRACTION38chain 'E' and (resid 182 through 215 )

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Yorodumi

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  • 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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