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- PDB-3krk: X-ray crystal structure of arachidonic acid bound in the cyclooxy... -

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Basic information

Entry
Database: PDB / ID: 3krk
TitleX-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of L531F murine COX-2
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / COX-2 / Dioxygenase / Disulfide bond / Endoplasmic reticulum / Fatty acid biosynthesis / Glycoprotein / Heme / Iron / Lipid synthesis / Membrane / Metal-binding / Microsome / Peroxidase / Phosphoprotein / Prostaglandin biosynthesis
Function / homology
Function and homology information


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of fever generation / response to selenium ion / cellular response to fluid shear stress / prostaglandin secretion / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / decidualization / nuclear outer membrane / brown fat cell differentiation / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / regulation of cell population proliferation / response to oxidative stress / cellular response to hypoxia / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain ...: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ARACHIDONIC ACID / ACRYLIC ACID / PROTOPORPHYRIN IX CONTAINING CO / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVecchio, A.J. / Simmons, D.M. / Malkowski, M.G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of fatty acid substrate binding to cyclooxygenase-2.
Authors: Vecchio, A.J. / Simmons, D.M. / Malkowski, M.G.
History
DepositionNov 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,23421
Polymers135,9352
Non-polymers5,30019
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-21 kcal/mol
Surface area42710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.790, 133.040, 180.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Prostaglandin G/H synthase 2 / Cyclooxygenase-2 / COX-2 / Prostaglandin-endoperoxide synthase 2 / Prostaglandin H2 synthase 2 / ...Cyclooxygenase-2 / COX-2 / Prostaglandin-endoperoxide synthase 2 / Prostaglandin H2 synthase 2 / PGH synthase 2 / PGHS-2 / PHS II / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / TIS10 protein / Macrophage activation-associated marker protein P71/73 / PES-2


Mass: 67967.406 Da / Num. of mol.: 2 / Fragment: UNP residues 20-604 / Mutation: L531F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cox-2, Cox2, Pghs-b, Ptgs2, Tis10 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

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Sugars , 4 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 643 molecules

#4: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O2
#5: Chemical
ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23-34% Polyacrylic acid 5100, 0.1M Hepes pH 7.5, 0.02M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2008
RadiationMonochromator: Asymmetric cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 55133 / Num. obs: 55133 / % possible obs: 96.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.1 / Num. unique all: 7387 / % possible all: 90.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CVU

1cvu


Resolution: 2.4→19.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.76 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.394 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2794 5.1 %RANDOM
Rwork0.17948 ---
all0.226 55143 --
obs0.1819 52249 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.99 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8899 0 359 632 9890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229582
X-RAY DIFFRACTIONr_angle_refined_deg1.471.99213030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05851113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94923.946446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.383151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4051545
X-RAY DIFFRACTIONr_chiral_restr0.1190.21393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217373
X-RAY DIFFRACTIONr_mcbond_it0.261.55547
X-RAY DIFFRACTIONr_mcangle_it0.52229007
X-RAY DIFFRACTIONr_scbond_it0.95734035
X-RAY DIFFRACTIONr_scangle_it1.6964.54017
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 205 -
Rwork0.226 3384 -
obs--86.82 %
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)
11.8799-0.5788-0.49270.4509-0.06291.8885-0.01460.0092-0.14770.1995-0.04270.03080.3783-0.11340.05730.3152-0.07580.00080.01880.00420.115726.81422.008956.8071
24.59220.7367-0.56263.65882.67382.22720.0710.6038-0.52930.76380.7763-1.24260.56750.4573-0.84720.42530.1629-0.21830.3106-0.16620.604545.13250.177462.4095
34.22821.6406-0.84571.0626-2.05689.2058-0.0617-0.1521-0.4096-0.0152-0.1205-0.31250.41630.41860.18210.1640.0801-0.06190.05620.02890.260859.053818.824164.451
42.29040.8361-0.24120.76760.441.53960.036-0.0574-0.1230.1088-0.0636-0.06390.15990.03230.02760.1002-0.01620.00610.0469-0.00890.077528.189118.97252.4193
50.84790.6638-0.2230.84440.11360.87850.0612-0.09150.0790.1576-0.02810.1340.09-0.08-0.03310.1249-0.02160.01670.1091-0.02240.123630.929728.243271.741
60.11060.34920.01211.73990.16060.9386-0.03180.00410.0998-0.11940.07920.0921-0.2004-0.0953-0.04730.05890.0024-0.0060.0941-0.02940.174636.986347.648152.3648
72.0369-1.43230.23294.3051-0.76561.68-0.0021-0.16860.17720.10180.14710.3592-0.189-0.2914-0.1450.10570.01360.02660.0996-0.03690.160732.515850.71761.9361
80.62470.2899-0.04660.8360.06921.16390.0137-0.0878-0.00860.09660.0063-0.1558-0.01350.1572-0.020.03630.00070.01050.1185-0.03290.146851.058736.596852.3581
90.4657-0.0079-0.20952.44451.40362.2317-0.0089-0.14630.07540.17930.01080.1569-0.0956-0.0119-0.0020.0702-0.00160.01150.1128-0.02060.081935.843239.50472.5605
100.86610.50380.07191.20020.01910.780.0426-0.14790.0520.1146-0.01140.01250.0647-0.0161-0.03120.06660.00090.01690.1154-0.02170.060635.026933.354273.0304
110.9730.4366-0.78740.9015-0.56631.57840.0096-0.1403-0.10750.1837-0.0024-0.07340.17690.1076-0.00720.1230.0054-0.02980.0806-0.00640.115240.443921.2167.1377
122.08730.3364-2.1480.4082-0.03012.49330.088-0.3103-0.12510.1756-0.0284-0.22910.05330.3462-0.05960.1026-0.0078-0.07240.1689-0.04150.175355.194943.293464.0958
131.1728-0.35580.12430.93890.16172.6506-0.03940.03840.03030.00220.1264-0.0277-0.18450.2976-0.0870.034-0.04010.04210.1356-0.03630.144159.037838.160830.6988
143.3778-2.7992-0.39849.4923-1.67363.6052-0.07740.1525-0.3160.7237-0.1344-0.45140.3480.40070.21180.17850.0419-0.0020.2674-0.08340.248866.889824.219329.1626
152.39410.9692-2.35371.8442-0.16212.7842-0.1524-0.1947-0.26080.1771-0.0604-0.31990.28020.22210.21280.10570.0712-0.020.11760.01010.241149.39725.509523.4112
160.02510.1911-0.01561.75130.25570.8086-0.0018-0.012-0.0347-0.02710.0088-0.1707-0.02420.212-0.0070.0699-0.0154-0.00410.11450.00240.142442.453434.529834.4727
170.93550.4066-0.15110.2352-0.05850.2758-0.03530.15680.1588-0.09940.06220.1034-0.10470.011-0.02690.1853-0.0342-0.0090.12930.00210.13334.556229.717814.8492
181.80020.4706-0.36270.1474-0.09960.07420.03230.08660.07470.0724-0.00170.0477-0.02-0.0174-0.03060.1829-0.03170.02340.0938-0.01980.132926.686226.687932.8928
191.3390.0192-0.12671.06070.11541.95670.00890.09230.1246-0.0010.04550.1402-0.0466-0.1935-0.05430.0401-0.010.00830.1092-0.02140.157211.585518.959230.5535
200.59070.2518-0.38130.33560.14271.2603-0.0530.077-0.09190.00520.0626-0.04310.17390.0733-0.00950.08030.0093-0.00190.053-0.01250.134832.870912.706233.4306
214.34710.13250.07561.2995-0.11851.2079-0.00690.20080.1009-0.19980.03520.20880.0968-0.1985-0.02840.1123-0.0069-0.02030.1488-0.00050.038817.795418.217711.4505
220.6160.53480.41850.52120.51460.8009-0.0490.090.0897-0.10540.06870.0505-0.11080.0022-0.01970.1403-0.03410.00450.11620.00110.090335.339431.053712.6825
230.95520.5566-0.44441.3712-0.72491.4657-0.03520.1917-0.0312-0.17250.069-0.1232-0.02660.0944-0.03390.0942-0.01170.02680.0946-0.04530.107844.121423.461318.5456
240.8150.27960.30711.2156-0.32352.7240.06930.1022-0.2627-0.08650.018-0.03440.34310.0104-0.08740.1152-0.0064-0.00610.0572-0.02670.126723.04243.811727.4408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 67
2X-RAY DIFFRACTION2A68 - 87
3X-RAY DIFFRACTION3A88 - 122
4X-RAY DIFFRACTION4A123 - 157
5X-RAY DIFFRACTION5A158 - 217
6X-RAY DIFFRACTION6A218 - 268
7X-RAY DIFFRACTION7A269 - 304
8X-RAY DIFFRACTION8A305 - 376
9X-RAY DIFFRACTION9A377 - 412
10X-RAY DIFFRACTION10A413 - 469
11X-RAY DIFFRACTION11A470 - 557
12X-RAY DIFFRACTION12A558 - 584
13X-RAY DIFFRACTION13B33 - 66
14X-RAY DIFFRACTION14B67 - 79
15X-RAY DIFFRACTION15B80 - 122
16X-RAY DIFFRACTION16B123 - 157
17X-RAY DIFFRACTION17B158 - 217
18X-RAY DIFFRACTION18B218 - 236
19X-RAY DIFFRACTION19B237 - 321
20X-RAY DIFFRACTION20B322 - 385
21X-RAY DIFFRACTION21B386 - 429
22X-RAY DIFFRACTION22B430 - 465
23X-RAY DIFFRACTION23B466 - 550
24X-RAY DIFFRACTION24B551 - 583

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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

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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

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