[English] 日本語
Yorodumi
- PDB-13df: Crystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 13df
TitleCrystal structure of covalent inhibitor 3-(2-chloroacetamido)-N-(3-methoxyphenyl)benzamide bound to Ubiquitin C-terminal Hydrolase-L3
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / UCHL3 / covalent inhibitor / chloroacetamide / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


deNEDDylase activity / protein deubiquitination / protein catabolic process / post-translational protein modification / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / peptidase activity / UCH proteinases / Neddylation / ubiquitin-dependent protein catabolic process ...deNEDDylase activity / protein deubiquitination / protein catabolic process / post-translational protein modification / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / peptidase activity / UCH proteinases / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein ubiquitination / Golgi apparatus / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
: / Ubiquitin carboxyl-terminal hydrolase isozyme L3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPannala, N. / Patel, R. / Flaherty, D. / Das, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2026
Title: Identification, optimization, and structural elucidation of chloroacetamide scaffold as covalent inhibitors for Ubiquitin C-terminal Hydrolase L3
Authors: Beeralingappa, N.C. / Lu, M. / Patel, R. / Pannala, N. / Dhiman, A. / Heil, B.N. / Imhoff, R.D. / Smith, E.G. / Bahler, M.B. / Marsden, H.L. / Allen-Petersen, B.L. / Wendt, M.K. / Das, C. / Flaherty, D.P.
History
DepositionApr 30, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L3
B: Ubiquitin carboxyl-terminal hydrolase isozyme L3
C: Ubiquitin carboxyl-terminal hydrolase isozyme L3
D: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55711
Polymers107,9944
Non-polymers1,5637
Water7,602422
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5094
Polymers26,9981
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4133
Polymers26,9981
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3172
Polymers26,9981
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin carboxyl-terminal hydrolase isozyme L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3172
Polymers26,9981
Non-polymers3191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.202, 85.305, 124.367
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase isozyme L3 / UCH-L3 / Ubiquitin thioesterase L3


Mass: 26998.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P15374, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-A1DFE / 3-(2-chloroacetamido)-N-(3-methoxyphenyl)benzamide


Mass: 318.755 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H15ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris Propane Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 164183 / % possible obs: 97.9 % / Redundancy: 6.4 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Χ2: 1.289 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.61.57884000.4910.8110.651.7090.92898.7
1.92-1.996.61.03884150.6950.9050.4271.1240.99798.5
1.99-2.086.50.71284270.8220.950.2960.7731.08598.6
2.08-2.196.50.47584630.9220.9790.1980.5161.12798.7
2.19-2.336.40.35983830.9420.9850.1510.391.43898.2
2.33-2.5160.25781940.9580.9890.1120.2811.46495.6
2.51-2.766.70.19383100.980.9950.080.211.56997.2
2.76-3.166.70.13185750.990.9970.0540.1421.76399.6
3.16-3.996.20.08685380.9920.9980.0380.0941.37898.9
3.99-506.20.05983600.9950.9990.0260.0651.13695.6

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→42.68 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 3894 2.37 %
Rwork0.1955 --
obs0.1965 164183 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6826 0 99 422 7347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097086
X-RAY DIFFRACTIONf_angle_d1.0969603
X-RAY DIFFRACTIONf_dihedral_angle_d7.172928
X-RAY DIFFRACTIONf_chiral_restr0.0641051
X-RAY DIFFRACTIONf_plane_restr0.0091257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.39891060.41064368X-RAY DIFFRACTION73
1.86-1.890.41361520.38675782X-RAY DIFFRACTION98
1.89-1.910.50781040.38825873X-RAY DIFFRACTION98
1.91-1.940.38621550.35675818X-RAY DIFFRACTION98
1.94-1.960.32121440.32055772X-RAY DIFFRACTION98
1.96-1.990.37791430.30455920X-RAY DIFFRACTION98
1.99-2.030.27541460.27575814X-RAY DIFFRACTION99
2.03-2.060.29831380.25945718X-RAY DIFFRACTION99
2.06-2.090.29571390.25416064X-RAY DIFFRACTION98
2.09-2.130.28581450.23545734X-RAY DIFFRACTION98
2.13-2.170.26271330.22635885X-RAY DIFFRACTION99
2.17-2.220.24141520.22765838X-RAY DIFFRACTION98
2.22-2.270.27741520.22915794X-RAY DIFFRACTION98
2.27-2.320.27231340.21365811X-RAY DIFFRACTION98
2.32-2.380.30631390.21755775X-RAY DIFFRACTION98
2.38-2.440.28971480.19735731X-RAY DIFFRACTION96
2.44-2.510.27631240.21335328X-RAY DIFFRACTION89
2.51-2.590.23421300.20285620X-RAY DIFFRACTION95
2.59-2.690.23651460.20335888X-RAY DIFFRACTION98
2.69-2.790.26581410.2045817X-RAY DIFFRACTION99
2.79-2.920.30041430.21025868X-RAY DIFFRACTION99
2.92-3.070.26611460.19365883X-RAY DIFFRACTION99
3.07-3.270.27541390.19125856X-RAY DIFFRACTION98
3.27-3.520.22831480.16745773X-RAY DIFFRACTION98
3.52-3.870.20841450.16425738X-RAY DIFFRACTION96
3.87-4.430.19511400.14395627X-RAY DIFFRACTION95
4.43-5.580.16881240.15965303X-RAY DIFFRACTION90
5.58-42.680.17811380.17635891X-RAY DIFFRACTION99
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)
14.0551.4194-0.22017.0004-0.65515.0910.01070.4681-0.06530.4636-0.05070.6045-0.0054-0.35740.00330.3596-0.08590.03030.5236-0.09030.390423.5234-0.7977-60.7718
24.30410.58480.46546.0323-1.56182.6618-0.33680.3336-0.2395-0.18510.26260.05130.4846-0.60060.12060.3633-0.08170.03450.4073-0.1110.275833.75-2.5025-64.8487
31.26190.4446-1.19191.99430.79693.7324-0.2250.0966-0.4032-0.0626-0.03890.04740.29830.02330.21580.2375-0.03940.01480.3527-0.00230.323136.7745-3.7227-56.1257
45.32856.453-2.24418.5255-2.07621.60480.0997-0.36120.37710.46910.0607-0.05860.110.2623-0.14660.22350.0319-0.04560.3102-0.01070.273137.855314.3106-40.6032
52.0323-0.66050.26124.07840.33953.35360.08930.10720.0671-0.0578-0.0525-0.0009-0.22950.0011-0.07250.1601-0.02290.00090.24610.03960.152834.275114.5878-58.0728
62.3715-0.5792-1.14975.19950.07933.10950.14890.4250.091-0.4295-0.04740.1091-0.0315-0.3118-0.08320.3315-0.0236-0.03310.44380.070.245130.291616.1639-66.9809
70.7322-0.0857-0.87713.23340.71493.3582-0.06930.10290.07080.07440.08210.05360.10550.0152-0.01090.157-0.0398-0.02520.24830.00360.179836.66368.9431-53.2552
84.3832-1.6367-5.40384.88731.74046.52970.1523-0.3319-0.10280.27170.2708-0.26680.26451.0212-0.2440.28170.0078-0.03360.39650.00460.343542.0079-0.558-50.6329
94.3331-0.3007-1.6625.3865-0.28412.8685-0.2-0.0485-0.60070.4909-0.15580.54990.0594-0.02240.38620.2339-0.02850.02830.2261-0.00970.373531.6921-2.3594-51.0274
105.05660.9271-4.13583.7403-1.08233.6289-0.1408-1.11830.2790.6392-0.14850.57160.3084-0.20280.28410.617-0.11480.00510.5051-0.02620.495618.318217.1184-16.9115
115.86540.9344-0.59844.7281-1.15973.7494-0.131-0.26550.10850.8052-0.0322-0.1654-0.3225-0.10410.1860.59950.0109-0.06650.2849-0.12620.411913.99530.3352-20.7242
122.9098-1.26390.27086.0188-0.17562.98670.104-0.08040.03620.84-0.23020.3311-0.0710.05420.06840.3199-0.04980.07030.2308-0.01780.280713.059918.7942-27.1401
133.5131-1.16912.74714.623-2.08257.25840.13420.3018-0.2849-0.0863-0.09890.39490.5705-0.0204-0.07630.2811-0.03540.03580.2732-0.060.37439.05787.6251-39.6123
142.9908-1.32811.13153.1196-0.3472.77760.01040.01030.4374-0.0212-0.0101-0.2172-0.28680.13960.01440.2504-0.07890.00670.25770.03380.367417.74625.1196-37.4358
154.66860.13960.44263.66091.03522.64180.19090.24621.2534-0.4063-0.0648-1.2579-1.00060.1712-0.08780.5124-0.07540.02820.3050.08730.77524.961835.3561-37.5748
162.8824-1.1364-0.64382.93410.04327.71490.1553-0.04440.45980.41770.1593-1.10.10050.8363-0.20530.3609-0.0529-0.02970.3633-0.02750.582429.005423.3067-36.491
171.889-0.7621-0.27442.6807-0.34572.1641-0.04820.11310.01540.1549-0.02540.0388-0.0779-0.02660.06460.1978-0.0368-0.01750.2047-0.00920.240712.152419.9516-34.2645
183.5587-1.33480.51752.3059-2.79634.1598-0.2542-0.108-0.06540.04750.35470.51410.1535-0.2376-0.10010.3277-0.02810.09350.2953-0.030.36493.200520.5441-27.7344
193.6367-0.6507-0.51693.3035-2.53754.1266-0.2714-0.0602-0.23790.32720.34790.45710.0871-0.01270.14730.3866-0.03320.0950.2849-0.0150.220411.068517.4739-21.8961
207.07920.6296-0.45686.1988-0.60294.59250.07090.34520.5194-0.23710.15460.6547-0.493-0.177-0.34140.47440.03410.13280.40380.12360.4901-5.15690.4006-7.1727
211.74122.39110.77956.88630.21121.2167-0.0416-0.24760.41260.88480.49140.0501-0.593-0.127-0.2520.79940.16740.30410.43060.0460.53940.34787.72893.6927
223.5856-0.2629-1.84023.2365-0.1424.59190.0968-0.3419-0.1763-0.1253-0.0125-0.460.12120.6424-0.0760.4640.01710.05070.3446-0.00140.414417.4457-6.75-5.6225
232.6730.3231-0.83124.78-0.41224.0681-0.1088-0.3008-0.07040.73540.06180.37450.3363-0.35720.04980.5479-0.00370.14810.31790.05570.29250.4321-12.78983.8911
242.13970.3073-1.16036.1104-2.20894.2449-0.1794-0.0382-0.5432-0.40190.34950.77240.9619-0.2080.01230.6212-0.03270.16340.29860.05430.4876-2.379-16.9432-5.0868
253.3284-0.7277-0.48894.8378-0.40613.0630.0874-0.1747-0.03620.1561-0.07570.00060.09750.1784-0.04770.4830.01450.06650.22080.01850.25569.1671-6.9003-2.6823
264.6916-3.7704-3.95197.42182.89386.3805-0.0297-0.95340.38611.41620.08890.227-0.56590.08980.02870.7031-0.1165-0.00810.5797-0.07760.357113.5614-1.16510.2128
274.1158-0.6924-1.10875.0873-1.23653.31450.0603-0.3310.46110.4029-0.035-0.284-0.22260.3431-0.1650.6058-0.02290.07690.2474-0.00820.366111.71444.2377-3.2386
285.27211.675-0.74844.0957-5.16687.46050.41180.68350.89230.8454-0.246-0.6699-0.0631.1008-0.25670.60170.1044-0.02980.4051-0.0320.770932.0064-20.814-30.7601
292.29670.8631-1.04212.24151.94093.83850.3240.1133-0.4190.71180.1632-0.47150.59840.7339-0.5060.98910.10010.08360.2975-0.04880.614426.4918-28.4702-35.6164
302.1925-0.27360.22363.77330.57612.3536-0.09650.1169-0.01710.312-0.10510.63430.3016-0.24410.20350.3959-0.08960.14230.2646-0.01460.415513.7023-15.6777-35.7098
312.33130.74050.54.23270.46493.056-0.0709-0.1831-0.43721.38010.00270.16871.3522-0.13710.01481.1699-0.07780.21960.26120.02880.537917.0914-25.8718-19.9309
322.0653-1.3005-1.2364.6280.56864.5146-0.2644-0.14730.0050.4250.1809-0.10250.51580.19050.03610.6255-0.06920.19850.2903-0.05990.451718.2804-18.2883-27.0493
333.3457-0.6575-0.38865.7716-0.21914.66640.15760.2085-0.2151-0.2257-0.22750.32850.5396-0.24980.08120.5496-0.07960.15150.3115-0.07030.391316.4929-19.4094-40.3132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 197 )
8X-RAY DIFFRACTION8chain 'A' and (resid 198 through 215 )
9X-RAY DIFFRACTION9chain 'A' and (resid 216 through 230 )
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 12 )
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 48 )
12X-RAY DIFFRACTION12chain 'B' and (resid 49 through 59 )
13X-RAY DIFFRACTION13chain 'B' and (resid 60 through 76 )
14X-RAY DIFFRACTION14chain 'B' and (resid 77 through 110 )
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 130 )
16X-RAY DIFFRACTION16chain 'B' and (resid 131 through 161 )
17X-RAY DIFFRACTION17chain 'B' and (resid 162 through 197 )
18X-RAY DIFFRACTION18chain 'B' and (resid 198 through 215 )
19X-RAY DIFFRACTION19chain 'B' and (resid 216 through 230 )
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 23 )
21X-RAY DIFFRACTION21chain 'C' and (resid 24 through 48 )
22X-RAY DIFFRACTION22chain 'C' and (resid 49 through 76 )
23X-RAY DIFFRACTION23chain 'C' and (resid 77 through 130 )
24X-RAY DIFFRACTION24chain 'C' and (resid 131 through 161 )
25X-RAY DIFFRACTION25chain 'C' and (resid 162 through 190 )
26X-RAY DIFFRACTION26chain 'C' and (resid 191 through 200 )
27X-RAY DIFFRACTION27chain 'C' and (resid 201 through 230 )
28X-RAY DIFFRACTION28chain 'D' and (resid 4 through 22 )
29X-RAY DIFFRACTION29chain 'D' and (resid 23 through 38 )
30X-RAY DIFFRACTION30chain 'D' and (resid 39 through 76 )
31X-RAY DIFFRACTION31chain 'D' and (resid 77 through 139 )
32X-RAY DIFFRACTION32chain 'D' and (resid 140 through 193 )
33X-RAY DIFFRACTION33chain 'D' and (resid 194 through 230 )

+
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