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Entry
Database: PDB / ID: 6lu7
TitleThe crystal structure of COVID-19 main protease in complex with an inhibitor N3
Components
  • 3C-like proteinase
  • N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
KeywordsVIRAL PROTEIN / protease
Function / homology
Function and homology information


modulation by virus of host autophagy / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / suppression by virus of host ISG15 activity ...modulation by virus of host autophagy / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / suppression by virus of host ISG15 activity / suppression by virus of host toll-like receptor signaling pathway / protein K48-linked deubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host IRF3 activity / exonuclease activity / suppression by virus of host NF-kappaB transcription factor activity / modulation by virus of host protein ubiquitination / transcription, RNA-templated / protein K63-linked deubiquitination / viral genome replication / positive stranded viral RNA replication / protein autoprocessing / suppression by virus of host TRAF activity / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA (nucleoside-2'-O-)-methyltransferase activity / host cell membrane / viral transcription / ubiquitinyl hydrolase 1 / helicase activity / cysteine-type peptidase activity / DNA helicase / methyltransferase activity / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / thiol-dependent deubiquitinase / host cell perinuclear region of cytoplasm / viral protein processing / methylation / RNA helicase / induction by virus of host autophagy / suppression by virus of host type I interferon-mediated signaling pathway / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / host cell cytoplasm / Hydrolases; Acting on ester bonds / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding
Macro domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase ...Macro domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / (+) RNA virus helicase core domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP1, betacoronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / Non-structural protein NSP9, coronavirus / Peptidase C16, coronavirus / RNA polymerase, N-terminal, coronaviral / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Peptidase S1, PA clan / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / RNA-directed RNA polymerase, C-terminal domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Non-structural protein 6, coronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Peptidase S1, PA clan, chymotrypsin-like fold / Papain-like viral protease, palm and finger domains, coronavirus / DNA/RNA polymerase superfamily / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Peptidase C30, domain 3, coronavirus / Yro2-like, 7TM domain / Macro domain-like / Papain-like protease, thumb domain superfamily, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / DNA2/NAM7 helicase-like, C-terminal / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Peptidase C30, coronavirus / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Replicase polyprotein 1ab / N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsLiu, X. / Zhang, B. / Jin, Z. / Yang, H. / Rao, Z.
Citation
Journal: Nature / Year: 2020
Title: Structure of Mprofrom SARS-CoV-2 and discovery of its inhibitors.
Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / ...Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / Liu, X. / Yang, X. / Bai, F. / Liu, H. / Liu, X. / Guddat, L.W. / Xu, W. / Xiao, G. / Qin, C. / Shi, Z. / Jiang, H. / Rao, Z. / Yang, H.
#1: Journal: Biorxiv / Year: 2020
Title: Structure of Mpro from COVID-19 virus and discovery of its inhibitors.
Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / ...Authors: Jin, Z. / Du, X. / Xu, Y. / Deng, Y. / Liu, M. / Zhao, Y. / Zhang, B. / Li, X. / Zhang, L. / Peng, C. / Duan, Y. / Yu, J. / Wang, L. / Yang, K. / Liu, F. / Jiang, R. / Yang, X. / You, T. / Liu, X. / Yang, X. / Bai, F. / Liu, H. / Liu, X. / Guddat, L. / Xu, W. / Xiao, G. / Qin, C. / Shi, Z. / Jiang, H. / Rao, Z. / Yang, H.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 12, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / software / struct / struct_conn / struct_site / struct_site_gen
Item: _citation.title / _entity.pdbx_number_of_molecules ..._citation.title / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.name / _software.version / _struct.title / _struct_conn.pdbx_dist_value
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Feb 19, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_abbrev / _citation.title / _struct.title
Revision 2.2Feb 26, 2020Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 2.3Mar 11, 2020Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen / struct
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.pdbx_descriptor
Revision 2.4Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.5Apr 22, 2020Group: Database references / Category: citation / citation_author
Revision 2.6May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct.pdbx_descriptor / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 2.7May 27, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 2.8Jun 10, 2020Group: Structure summary / Category: entity / Item: _entity.pdbx_ec
Revision 2.9Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / citation_author ...atom_site / citation_author / entity / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / refine / refine_hist / reflns_shell / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _citation_author.identifier_ORCID / _entity.pdbx_fragment / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _struct_conn.pdbx_dist_value
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 3.1Mar 10, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity_name_com.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
C: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)34,5062
Polymers34,5062
Non-polymers00
Water1,51384
1
A: 3C-like proteinase
C: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE

A: 3C-like proteinase
C: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Theoretical massNumber of molelcules
Total (without water)69,0134
Polymers69,0134
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5190 Å2
ΔGint-27 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)97.931, 79.477, 51.803
Angle α, β, γ (deg.)90.000, 114.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-473-

HOH

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Components

#1: Protein 3C-like proteinase / pp1ab / ORF1ab polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / ...pp1ab / ORF1ab polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1 / Fragment: 3C-like proteinase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Protein/peptide N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE


Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: 2% polyethylene glycol (PEG) 6000, 3% DMSO, 1mM DTT, 0.1M MES buffer (pH 6.0), protein concentration 5mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0718 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.16→42.29 Å / Num. obs: 19455 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 6.3
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.472 / Num. unique obs: 1431 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HOB
Resolution: 2.16→27.81 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 997 5.13 %
Rwork0.202 18435 -
Obs0.204 19432 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.99 Å2 / Biso mean: 42.82 Å2 / Biso min: 16.91 Å2
Refinement stepCycle: final / Resolution: 2.16→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 21 84 2500
Biso mean--36.18 44.27 -
Num. residues----310
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.270.29691390.26172568270797
2.27-2.410.27421480.245626102758100
2.41-2.60.27481230.233326622785100
2.6-2.860.26281340.23226442778100
2.86-3.270.24081580.216326162774100
3.27-4.120.22611480.189726462794100
4.12-27.810.20491470.172526892836100

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