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- PDB-6myp: Avian mitochondrial complex II with TTFA (thenoyltrifluoroacetone... -

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Basic information

Entry
Database: PDB / ID: 6myp
TitleAvian mitochondrial complex II with TTFA (thenoyltrifluoroacetone) bound
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b, large subunit
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Complex II / membrane protein / heme protein / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Citric acid cycle (TCA cycle) / The tricarboxylic acid cycle / : / succinate metabolic process / succinate dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity ...Citric acid cycle (TCA cycle) / The tricarboxylic acid cycle / : / succinate metabolic process / succinate dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding
Similarity search - Function
Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / BICARBONATE ION / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / OXALOACETATE ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER ...1,2-Distearoyl-sn-glycerophosphoethanolamine / BICARBONATE ION / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / OXALOACETATE ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / 4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE / Unknown ligand / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBerry, E.A. / Huang, L.-S.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)1R01GM062563 United States
Citation
Journal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: Crystallographic investigation of the ubiquinone binding site of respiratory Complex II and its inhibitors.
Authors: Huang, L.S. / Lummen, P. / Berry, E.A.
#1: Journal: J. Biol. Chem. / Year: 2006
Title: 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
Authors: Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
#2: Journal: Biochim. Biophys. Acta / Year: 2006
Title: Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the "oxaloacetate-inhibited" state.
Authors: Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A.
Authors: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A.
#4: Journal: Cell / Year: 2005
Title: Crystal structure of mitochondrial respiratory membrane protein complex II.
Authors: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z.
History
DepositionNov 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 7, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b, large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,04480
Polymers123,3054
Non-polymers10,73976
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33710 Å2
ΔGint-120 kcal/mol
Surface area37890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.951, 84.303, 290.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial


Mass: 68256.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: heart
References: UniProt: F1NPJ4, UniProt: Q9YHT1*PLUS, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 28685.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: heart / References: UniProt: Q9YHT2, succinate dehydrogenase
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Succinate dehydrogenase complex subunit D / Succinate-ubiquinone oxidoreductase cytochrome b ...CybS / Succinate dehydrogenase complex subunit D / Succinate-ubiquinone oxidoreductase cytochrome b small subunit / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 10971.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: heart / References: UniProt: Q5ZIS0

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Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase cytochrome b, large subunit


Mass: 15391.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: heart
References: UniProt: D0VWW3, UniProt: A0A3Q2U2Y6*PLUS, succinate dehydrogenase

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Non-polymers , 15 types, 513 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 106.120 Da / Num. of mol.: 63 / Source method: obtained synthetically
#12: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#13: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#14: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#15: Chemical ChemComp-TTF / 4,4,4-TRIFLUORO-1-THIEN-2-YLBUTANE-1,3-DIONE / 2-THENOYLTRIFLUOROACETONE


Mass: 222.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H5F3O2S / Comment: inhibitor*YM
#16: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#17: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#18: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 48 g/L PEG3350, 15 mL/L PEG400, 24 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 1.6 mM manganese chloride, 0.64 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 ...Details: 48 g/L PEG3350, 15 mL/L PEG400, 24 mL/L isopropanol, 0.05 M HEPES sodium, 0.01 M Tris-HCl, 1.6 mM manganese chloride, 0.64 mM magnesium chloride, 1.5 mM sodium azide, 0.25 mM sodium EDTA, 10 g/L octyl beta-D-glucoside, undecyl-beta-D-maltoside, TTFA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9743 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2004
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9743 Å / Relative weight: 1
ReflectionResolution: 2.1→50.36 Å / Num. obs: 100834 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 6.9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(DEV_3150: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YQ3

1yq3


Resolution: 2.1→50.36 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.97
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2048 2.04 %Random
Rwork0.235 ---
obs0.235 100591 99.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.7618 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 470 437 9406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029131
X-RAY DIFFRACTIONf_angle_d0.5112297
X-RAY DIFFRACTIONf_dihedral_angle_d8.2955384
X-RAY DIFFRACTIONf_chiral_restr0.0381326
X-RAY DIFFRACTIONf_plane_restr0.0031536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14890.36241390.34486489X-RAY DIFFRACTION99
2.1489-2.20260.41551350.32916472X-RAY DIFFRACTION99
2.2026-2.26210.32361490.32126472X-RAY DIFFRACTION99
2.2621-2.32870.40141440.31386474X-RAY DIFFRACTION99
2.3287-2.40390.35391290.30176485X-RAY DIFFRACTION99
2.4039-2.48980.30571230.28786502X-RAY DIFFRACTION99
2.4898-2.58950.33671320.28326487X-RAY DIFFRACTION99
2.5895-2.70730.35171280.27536526X-RAY DIFFRACTION99
2.7073-2.850.34411290.26576524X-RAY DIFFRACTION99
2.85-3.02860.31931520.26336586X-RAY DIFFRACTION100
3.0286-3.26240.28081360.24846569X-RAY DIFFRACTION100
3.2624-3.59060.2711110.2326622X-RAY DIFFRACTION100
3.5906-4.110.21571580.20996655X-RAY DIFFRACTION100
4.11-5.17730.1831360.19296717X-RAY DIFFRACTION100
5.1773-50.37050.19571470.18486963X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 20.3751 Å / Origin y: 18.9961 Å / Origin z: 110.21 Å
111213212223313233
T0.3378 Å20.039 Å2-0.036 Å2-0.3864 Å20.0114 Å2--0.3938 Å2
L0.6086 °2-0.123 °20.5402 °2-0.591 °2-0.4126 °2--1.7345 °2
S-0.0082 Å °-0.1194 Å °-0.056 Å °-0.0463 Å °-0.0448 Å °-0.0203 Å °0.0998 Å °0.2805 Å °-0.0014 Å °
Refinement TLS groupSelection details: ALL

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