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- PDB-2at1: CRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOA... -

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Entry
Database: PDB / ID: 2at1
TitleCRYSTAL STRUCTURES OF PHOSPHONOACETAMIDE LIGATED T AND PHOSPHONOACETAMIDE AND MALONATE LIGATED R STATES OF ASPARTATE CARBAMOYLTRANSFERASE AT 2.8-ANGSTROMS RESOLUTION AND NEUTRAL PH
Components
  • ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
  • ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
KeywordsTRANSFERASE (CARBAMOYL-P / ASPARTATE)
Function / homology
Function and homology information


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / PHOSPHONOACETAMIDE / Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsGouaux, J.E. / Lipscomb, W.N.
Citation
Journal: Biochemistry / Year: 1990
Title: Crystal structures of phosphonoacetamide ligated T and phosphonoacetamide and malonate ligated R states of aspartate carbamoyltransferase at 2.8-A resolution and neutral pH.
Authors: Gouaux, J.E. / Lipscomb, W.N.
#1: Journal: Biochemistry / Year: 1990
Title: Structural Consequences of Effector Binding to the T State of Aspartate Carbamoyltransferase. Crystal Structures of the Unligated and ATP-, and Ctp-Complexed Enzymes at 2.6-Angstroms Resolution
Authors: Stevens, R.C. / Gouaux, J.E. / Lipscomb, W.N.
#2: Journal: Biochemistry / Year: 1990
Title: Crystal Structures of Aspartate Carbamoyltransferase Ligated with Phosphonoacetamide, Malonate, and Ctp or ATP at 2.8-Angstroms Resolution and Neutral Ph
Authors: Gouaux, J.E. / Stevens, R.C. / Lipscomb, W.N.
#3: Journal: Biochemistry / Year: 1989
Title: Structure of a Single Amino Acid Mutant of Aspartate Carbamoyltransferase at 2.5-Angstroms Resolution. Implications for the Cooperative Mechanism
Authors: Gouaux, J.E. / Lipscomb, W.N. / Middleton, S.A. / Kantrowitz, E.R.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1989
Title: Structural Transitions in Crystals of Native Aspartate Carbamoyltransferase
Authors: Gouaux, J.E. / Lipscomb, W.N.
#5: Journal: J.Mol.Biol. / Year: 1988
Title: Complex of N-Phosphonacetyl-L-Aspartate with Aspartate Carbamoyltransferase. X-Ray Refinement, Analysis of Conformational Changes and Catalytic and Allosteric Mechanisms
Authors: Ke, H. / Lipscomb, W.N. / Cho, Y. / Honzatko, R.B.
#6: Journal: Science / Year: 1988
Title: Escherichia Coli Aspartate Transcarbamylase. The Relation between Structure and Function
Authors: Kantrowitz, E.R. / Lipscomb, W.N.
#7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Three-Dimensional Structure of Carbamoyl Phosphate and Succinate Bound to Aspartate Carbamoyltransferase
Authors: Gouaux, J.E. / Lipscomb, W.N.
#8: Journal: J.Mol.Biol. / Year: 1987
Title: Structural Asymmetry in the Ctp-Liganded Form of Aspartate Carbamoyltransferase from Escherichia Coli
Authors: Kim, K.H. / Pan, Z. / Honzatko, R.B. / Ke, H. / Lipscomb, W.N.
#9: Journal: J.Mol.Biol. / Year: 1987
Title: 2.5 Angstroms Structure of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analog N-(Phosphonacetyl)-L-Aspartate
Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N.
#10: Journal: Biochem.Biophys.Res.Commun. / Year: 1987
Title: The Catalytic Mechanism of Escherichia Coli Aspartate Carbamoyltransferase. A Molecular Modelling Study
Authors: Gouaux, J.E. / Krause, K.L. / Lipscomb, W.N.
#11: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: Structure at 2.9-Angstroms Resolution of Aspartate Carbamoyltransferase Complexed with the Bisubstrate Analogue N-(Phosphonacetyl)-L-Aspartate
Authors: Krause, K.L. / Volz, K.W. / Lipscomb, W.N.
#12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structure of Unligated Aspartate Carbamoyltransferase of Escherichia Coli at 2.6-Angstroms Resolution
Authors: Ke, H. / Honzatko, R.B. / Lipscomb, W.N.
#13: Journal: J.Mol.Biol. / Year: 1982
Title: Crystal and Molecular Structures of Native and Ctp-Liganded Aspartate Carbamoyltransferase from Escherichia Coli
Authors: Honzatko, R.B. / Crawford, J.L. / Monaco, H.L. / Ladner, J.E. / Edwards, B.F.P. / Evans, D.R. / Warren, S.G. / Wiley, D.C. / Ladner, R.C. / Lipscomb, W.N.
#14: Journal: J.Mol.Biol. / Year: 1982
Title: Interactions of Phosphate Ligands with Escherichia Coli Aspartate Carbamoyltransferase in the Crystalline State
Authors: Honzatko, R.B. / Lipscomb, W.N.
#15: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Interactions of Metal-Nucleotide Complexes with Aspartate Carbamoyltransferase in the Crystalline State
Authors: Honzatko, R.B. / Lipscomb, W.N.
#16: Journal: Proc.Natl.Acad.Sci.USA / Year: 1982
Title: Gross Quaternary Changes in Aspartate Carbamoyltransferase are Induced by the Binding of N-(Phosphonacetyl)-L-Aspartate. A 3.5-Angstroms Resolution Study
Authors: Ladner, J.E. / Kitchell, J.P. / Honzatko, R.B. / Ke, H.M. / Volz, K.W. / Kalb(Gilboa), A.J. / Ladner, R.C. / Lipscomb, W.N.
#17: Journal: Proc.Natl.Acad.Sci.USA / Year: 1979
Title: A 3.0-Angstroms Resolution Study of Nucleotide Complexes with Aspartate Carbamoyltransferase
Authors: Honzatko, R.B. / Monaco, H.L. / Lipscomb, W.N.
#18: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Three-Dimensional Structures of Aspartate Carbamoyltransferase from Escherichia Coli and of its Complex with Cytidine Triphosphate
Authors: Monaco, H.L. / Crawford, J.L. / Lipscomb, W.N.
#19: Journal: STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN
Year: 1975
Title: Binding Site at 5.5 Angstroms Resolution of Cytidine Triphosphate, the Allosteric Inhibitor of Aspartate Transcarbamylase from Escherichia Coli. Relation to Mechanisms of Control
Authors: Lipscomb, W.N. / Edwards, B.F.P. / Evans, D.R. / Pastra-Landis, S.C.
#20: Journal: Proc.Natl.Acad.Sci.USA / Year: 1973
Title: Aspartate Transcarbamoylase from Escherichia Coli. Electron Density at 5.5 Angstroms Resolution
Authors: Warren, S.G. / Edwards, B.F.P. / Evans, D.R. / Wiley, D.C. / Lipscomb, W.N.
History
DepositionSep 22, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
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.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,91310
Polymers102,8194
Non-polymers1,0946
Water0
1
A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules

A: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
B: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
C: ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN
D: ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,73830
Polymers308,45812
Non-polymers3,28118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area31760 Å2
ΔGint-119 kcal/mol
Surface area100900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.200, 122.200, 156.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: RESIDUES PRO A 268 AND PRO C 268 ARE CIS-PROLINES.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.109515, -0.993509, 0.030771), (-0.993693, 0.108679, -0.027637), (0.024113, -0.033603, -0.999144)
Vector: 102.2125, 92.5902, 80.2247)
DetailsTHE ENZYME IS A DODECAMER COMPOSED OF SIX CATALYTIC CHAINS AND SIX REGULATORY CHAINS THAT CAN BE DISSOCIATED INTO SUBUNITS. THE ASYMMETRIC UNIT OF THE CRYSTAL CONSISTS OF ONE THIRD OF THE MOLECULE - TWO CATALYTIC AND TWO REGULATORY CHAINS. CHAINS *A* AND *C* (REFERRED TO AS C1 AND C6 RESPECTIVELY IN THE *JRNL* REFERENCE ABOVE) ARE THE CATALYTIC CHAINS CONSISTING OF 310 RESIDUES EACH. CHAINS *B* AND *D* (REFERRED TO AS R1 AND R6 RESPECTIVELY IN THE *JRNL* REFERENCE ABOVE) ARE THE REGULATORY CHAINS CONSISTING OF 153 RESIDUES EACH. THE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS, WHICH IS SPECIFIED ON THE *MTRIX* RECORDS BELOW, RELATES THE *A* AND *B* CHAINS TO THE *C* AND *D* CHAINS.

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Components

#1: Protein ASPARTATE CARBAMOYLTRANSFERASE (R STATE), CATALYTIC CHAIN


Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein ASPARTATE CARBAMOYLTRANSFERASE REGULATORY CHAIN


Mass: 17072.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7F3
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
#4: Chemical ChemComp-PCT / PHOSPHONOACETAMIDE


Mass: 139.047 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO4P
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal grow
*PLUS
pH: 5.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlenzyme11
220 mMPAM11
320 mMmalonate11
43 mMsodium azide11

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Num. obs: 22862 / % possible obs: 79 % / Num. measured all: 58554 / Rmerge(I) obs: 0.067

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.17
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 32 0 7138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection obs: 20174 / σ(I): 2 / Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d

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