[English] 日本語
Yorodumi
- PDB-4mds: Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mds
TitleDiscovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: identification of ML300 and non-covalent nanomolar inhibitors with an induced-fit binding
Components3C-like proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / chymotrypsin-like / protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Trypsin-like serine proteases / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-23H / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsMesecar, A.D. / Grum-Tokars, V.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and ...Title: Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding.
Authors: Turlington, M. / Chun, A. / Tomar, S. / Eggler, A. / Grum-Tokars, V. / Jacobs, J. / Daniels, J.S. / Dawson, E. / Saldanha, A. / Chase, P. / Baez-Santos, Y.M. / Lindsley, C.W. / Hodder, P. / ...Authors: Turlington, M. / Chun, A. / Tomar, S. / Eggler, A. / Grum-Tokars, V. / Jacobs, J. / Daniels, J.S. / Dawson, E. / Saldanha, A. / Chase, P. / Baez-Santos, Y.M. / Lindsley, C.W. / Hodder, P. / Mesecar, A.D. / Stauffer, S.R.
History
DepositionAug 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1444
Polymers33,4721
Non-polymers6723
Water7,963442
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2888
Polymers66,9442
Non-polymers1,3446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2960 Å2
ΔGint-6 kcal/mol
Surface area26510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.824, 56.244, 53.140
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

-
Components

#1: Protein 3C-like proteinase / 3CL protease / 3CL-PRO / 3CLp / nsp5


Mass: 33472.184 Da / Num. of mol.: 1 / Fragment: UNP residues 3241-3542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Gene: 1a / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-23H / N-[4-(acetylamino)phenyl]-2-(1H-benzotriazol-1-yl)-N-[(1R)-2-[(2-methylbutan-2-yl)amino]-1-(1-methyl-1H-pyrrol-2-yl)-2-oxoethyl]acetamide


Mass: 515.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33N7O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1:1 ratio of enzyme (incubated on ice with 1 mM inhibitor) to crystallization solution (14.5% PEG20000, 50 mM MES, pH 6.0, 50 mM potassium chloride, 1% MPD), VAPOR DIFFUSION, HANGING DROP, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.598→55.419 Å / Num. all: 43365 / Num. obs: 41370 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.598 Å

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.598→55.419 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.579 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21227 2081 5 %RANDOM
Rwork0.1699 ---
obs0.172 39272 95.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å21.15 Å2
2---0.69 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.598→55.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 46 442 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222487
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9693391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0615318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2624.299107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11815400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4331512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21104
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21722
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3060.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7621.51572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09722492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.95731050
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8654.5894
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 105 -
Rwork0.227 2185 -
obs--71.52 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.70233.9999-0.75973.5986-0.62520.21590.0505-0.0883-0.2543-0.0299-0.0033-0.156-0.08190.0986-0.04720.0718-0.00130.01830.09550.00420.11918.84319.4193-21.7807
24.2818-0.42030.07892.67370.37430.5790.1090.0382-0.3632-0.0295-0.06290.23710.0718-0.0997-0.04610.0593-0.0239-0.01690.03490.01870.1051-11.48811.3916-20.7093
35.3806-2.3380.018611.2476-7.73812.90560.1089-0.3373-0.21120.07110.26421.13070.1745-0.9549-0.37310.0629-0.070.0180.1787-0.0040.2837-24.98116.6365-16.4553
415.28632.53310.97863.5401-0.7080.72680.04930.02920.2519-0.14860.07890.27350.2612-0.13-0.12820.0981-0.0275-0.0440.04240.00010.224-16.4654-5.5176-23.0992
51.6546-1.1154-0.0039.064.06983.06840.2145-0.1202-0.35080.04010.0097-0.09390.1359-0.0098-0.22420.086-0.0433-0.01390.08540.04540.2113-11.744-4.0177-17.1733
63.392-1.4888-0.25695.15680.89730.85920.179-0.1327-0.46760.260.0047-0.39980.10370.0178-0.18370.1002-0.0311-0.03880.0590.11080.1487-0.4874-2.3435-13.5913
72.27871.71051.59024.41472.04534.14590.1305-0.1288-0.1640.1522-0.0426-0.1727-0.0007-0.009-0.08790.032-0.00880.01870.04490.00420.03381.353813.6484-17.5759
80.71230.5419-0.06031.90960.53990.7491-0.0391-0.0204-0.1826-0.14160.05150.0042-0.10350.0846-0.01240.0913-0.01170.00880.0974-0.01660.0480.751614.8385-21.3259
91.95810.92611.54465.91116.481115.3970.11910.01880.0226-0.0468-0.01450.12410.0038-0.0059-0.10460.05150.00850.00130.04760.0160.0054-4.884718.5293-21.591
109.76350.45025.30394.8402-0.5145.51660.2105-0.063-0.7330.218-0.0042-0.74720.07590.2747-0.20630.0410.0002-0.00770.05020.0250.16394.42367.2522-16.5364
112.6255-0.18550.52263.0526-0.02841.5580.049-0.1143-0.08190.0083-0.0051-0.0082-0.0752-0.1014-0.04390.0384-0.01020.01940.04910.0150.0026-5.458314.3402-17.8941
122.74181.56610.59663.52590.46120.90340.0428-0.2550.23410.1756-0.14810.4161-0.0441-0.12790.10530.0767-0.01630.04120.1092-0.01250.0424-11.777817.533-12.5577
139.4886-1.3238-1.08852.61091.02981.3477-0.07930.50070.3712-0.10040.0585-0.2978-0.11830.23480.02080.1205-0.07210.01090.13730.03530.030115.012428.3533-12.0559
1421.82155.7434-8.733720.2379-1.79895.0420.0115-0.4711.05960.18560.1985-0.6361-0.6420.9937-0.210.2901-0.14090.00590.2290.07860.340522.466637.9692-12.5495
157.2119-3.07696.4376.8367-0.702814.4281-0.2723-0.21540.71730.67410.1583-0.3087-0.74190.31650.1140.4305-0.0584-0.07760.1030.00580.19538.017140.0486-3.4218
166.0849-2.53296.32054.2259-3.40016.7518-0.1297-0.41880.13220.19050.07860.1981-0.1-0.22130.05120.2271-0.01690.02720.16630.02110.04037.295329.5825-1.7065
174.3492-2.19911.57315.3688-0.76335.1738-0.18610.03690.55750.23460.0019-0.5278-0.31070.59860.18420.161-0.0929-0.03820.18920.00840.126818.303531.5133-5.1853
186.2829-2.9679-2.46698.60411.71773.26440.02750.51750.5627-1.05460.0972-0.4789-0.6326-0.105-0.12470.4681-0.08670.02510.22160.11120.225414.370238.3066-19.3396
1914.0064-3.04943.02853.9492-1.07176.0043-0.07370.6174-0.3144-0.06950.0207-0.07560.09930.35390.0530.1011-0.08540.02920.1395-0.02720.004611.824222.6963-13.2421
2025.52483.3384-0.943214.58240.728341.96410.639-1.0277-1.0420.1721-0.0823-1.70731.54494.1401-0.55660.22250.15030.02150.6195-0.04240.283321.41316.147-14.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 46
3X-RAY DIFFRACTION3A47 - 59
4X-RAY DIFFRACTION4A60 - 71
5X-RAY DIFFRACTION5A72 - 88
6X-RAY DIFFRACTION6A89 - 106
7X-RAY DIFFRACTION7A107 - 118
8X-RAY DIFFRACTION8A119 - 133
9X-RAY DIFFRACTION9A134 - 142
10X-RAY DIFFRACTION10A143 - 155
11X-RAY DIFFRACTION11A156 - 173
12X-RAY DIFFRACTION12A174 - 198
13X-RAY DIFFRACTION13A199 - 215
14X-RAY DIFFRACTION14A216 - 222
15X-RAY DIFFRACTION15A223 - 238
16X-RAY DIFFRACTION16A239 - 247
17X-RAY DIFFRACTION17A248 - 271
18X-RAY DIFFRACTION18A272 - 286
19X-RAY DIFFRACTION19A287 - 297
20X-RAY DIFFRACTION20A298 - 303

+
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