[English] 日本語
Yorodumi
- PDB-4ph9: The structure of Ibuprofen bound to cyclooxygenase-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ph9
TitleThe structure of Ibuprofen bound to cyclooxygenase-2
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE / membrane protein / cyclooxygenase / COX / COX-2 / Ibuprofen / monotopic / prostaglandin / NSAID
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 / response to selenium ion / positive regulation of fever generation / prostaglandin secretion / cellular response to fluid shear stress / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / nuclear outer membrane / decidualization / 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 / cellular response to hypoxia / response to oxidative stress / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
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
ACRYLIC ACID / PROTOPORPHYRIN IX CONTAINING FE / IBUPROFEN / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsOrlando, B.J. / Lucido, M.J. / Malkowski, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM077176 United States
CitationJournal: J.Struct.Biol. / Year: 2015
Title: The structure of ibuprofen bound to cyclooxygenase-2.
Authors: Orlando, B.J. / Lucido, M.J. / Malkowski, M.G.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 7, 2015Group: Database references
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Nov 22, 2017Group: Refinement description / Category: software
Revision 2.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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_struct_conn_angle / refine_hist / struct_asym / struct_conn / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,63832
Polymers126,9212
Non-polymers5,71730
Water20,3031127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16590 Å2
ΔGint47 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.941, 132.228, 180.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 63460.406 Da / Num. of mol.: 2 / Fragment: UNP residues 20-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05769, prostaglandin-endoperoxide synthase

-
Sugars , 4 types, 9 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.: 2 / Source method: obtained synthetically
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: obtained synthetically
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
#6: 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.: 3 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#7: 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.: 3 / Source method: obtained synthetically / 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

-
Non-polymers , 5 types, 1148 molecules

#4: Chemical ChemComp-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID


Mass: 206.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18O2 / Comment: antiinflammatory, medication*YM
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical
ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O2
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1127 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.28 % / Description: rectangular
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23-34% PAA-5100, 100mM HEPES (pH 7.5), 20mM MgCl2, 0.6% BoG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 12, 2012
RadiationMonochromator: Horizontal focusing 5.05iN asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 1.81→40 Å / Num. all: 128926 / Num. obs: 128926 / % possible obs: 98.43 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 24.49 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.044 / Net I/av σ(I): 22.395 / Net I/σ(I): 13.6 / Num. measured all: 605910
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.81-1.8752.490.40372.4958351.08990.8
1.84-1.872.70.38460201.09792.8
1.87-1.9130.33161331.09294.8
1.91-1.953.50.25562681.09296.4
1.95-1.994.10.2264121.07698.8
1.99-2.044.40.18564761.04899.9
2.04-2.094.70.16665211.091100
2.09-2.155.20.14464721.087100
2.15-2.215.20.1265051.065100
2.21-2.285.20.10665351.061100
2.28-2.365.30.09565151.09799.9
2.36-2.465.30.08265291.04999.9
2.46-2.575.30.07465231.02999.9
2.57-2.75.40.0676547199.9
2.7-2.875.40.05965211.0499.9
2.87-3.095.40.05365671.00299.9
3.09-3.415.40.04965531.09399.9
3.41-3.950.03565950.95499.6
3.9-4.915.30.04366440.96599.7
4.91-405.20.04467600.9898.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.79 Å38.56 Å
Translation6.79 Å38.56 Å

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
HKL-2000v704udata collection
HKL-2000v704udata reduction
PHASER2.5.6phasing
PDB_EXTRACT3.14data extraction
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HS5

3hs5


Resolution: 1.81→35.55 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 22.47
RfactorNum. reflection% reflectionSelection details
Rfree0.197 6401 4.99 %Random selection
Rwork0.16 ---
obs0.162 128316 98 %-
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.97 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: final / Resolution: 1.81→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 72 1128 10144
Biso mean--37.6 39.34 -
Num. residues----1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139687
X-RAY DIFFRACTIONf_angle_d1.3113131
X-RAY DIFFRACTIONf_dihedral_angle_d14.9293656
X-RAY DIFFRACTIONf_chiral_restr0.0611378
X-RAY DIFFRACTIONf_plane_restr0.0071676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.83110.26422020.23663565X-RAY DIFFRACTION88
1.8311-1.85270.26481700.22853800X-RAY DIFFRACTION92
1.8527-1.87530.29451750.22073845X-RAY DIFFRACTION93
1.8753-1.8990.24171800.21023923X-RAY DIFFRACTION95
1.899-1.9240.26141570.20223950X-RAY DIFFRACTION95
1.924-1.95030.25522260.19363970X-RAY DIFFRACTION96
1.9503-1.97820.23062180.18854030X-RAY DIFFRACTION98
1.9782-2.00770.24142110.17924087X-RAY DIFFRACTION99
2.0077-2.03910.22662120.17994107X-RAY DIFFRACTION100
2.0391-2.07250.21572420.17864082X-RAY DIFFRACTION100
2.0725-2.10830.19952160.1774101X-RAY DIFFRACTION99
2.1083-2.14660.22712050.17264098X-RAY DIFFRACTION100
2.1466-2.18790.21952250.17294122X-RAY DIFFRACTION99
2.1879-2.23250.24672340.17114076X-RAY DIFFRACTION99
2.2325-2.28110.21982270.16794075X-RAY DIFFRACTION99
2.2811-2.33410.22282000.16624085X-RAY DIFFRACTION99
2.3341-2.39250.20582040.16354127X-RAY DIFFRACTION99
2.3925-2.45710.21632330.16634074X-RAY DIFFRACTION99
2.4571-2.52940.21062250.16244080X-RAY DIFFRACTION99
2.5294-2.6110.22012160.17244100X-RAY DIFFRACTION99
2.611-2.70430.20192510.16834109X-RAY DIFFRACTION99
2.7043-2.81260.19442430.15924061X-RAY DIFFRACTION99
2.8126-2.94050.21892310.16514118X-RAY DIFFRACTION99
2.9405-3.09550.22622240.16854129X-RAY DIFFRACTION99
3.0955-3.28930.19452230.1594152X-RAY DIFFRACTION100
3.2893-3.5430.18152400.14864121X-RAY DIFFRACTION99
3.543-3.89920.16392350.13594149X-RAY DIFFRACTION99
3.8992-4.46250.16322190.12884188X-RAY DIFFRACTION100
4.4625-5.61860.15931940.13294258X-RAY DIFFRACTION100
5.6186-35.56040.1541630.16314333X-RAY DIFFRACTION97
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)
10.0065-0.01610.05430.0611-0.13670.47990.06650.1232-0.1043-0.3017-0.02640.06480.52270.0322-0.01810.4990.0122-0.04880.2281-0.02910.303927.67070.850732.201
20.17550.0645-0.06660.08280.07610.19450.05820.0412-0.2399-0.0238-0.00690.15860.2591-0.1278-0.01030.2475-0.0659-0.0630.271-0.01650.31885.024617.662827.39
30.16170.0716-0.00540.1280.03050.06980.06640.1187-0.0124-0.1344-0.0818-0.02170.18850.1159-0.00620.25090.08840.01180.22090.00960.17436.121819.631125.511
40.1046-0.1312-0.00510.1848-0.03840.07980.05470.13680.0134-0.1141-0.05150.01550.04940.047500.20480.0167-0.00130.23360.02230.210123.930634.481226.5913
50.4015-0.2283-0.07190.6159-0.09130.81090.05050.10420.037-0.08590.00610.02620.0435-0.0430.00050.13150.0096-0.00620.16490.02530.159518.885736.180227.4132
60.0703-0.02590.02290.0119-0.0410.4456-0.0268-0.1337-0.07330.09990.10420.1676-0.1005-0.3621-0.00520.2040.02190.04620.34250.06360.3313-0.388532.464660.9339
70.0875-0.0239-0.03890.07180.05540.0629-0.0196-0.0216-0.11160.03430.01250.2030.0875-0.17-0.00760.2327-0.04060.03090.23920.0380.335212.46716.375166.175
80.3323-0.12990.03340.2427-0.08680.1809-0.0545-0.09740.03050.09070.0645-0.0055-0.0812-0.024800.19960.02720.00850.19230.00180.188124.380231.81667.6662
90.4799-0.2147-0.07440.3949-0.15620.38630.0378-0.04740.0237-0.0399-0.0263-0.0670.09840.095300.17390.01620.0080.17780.00650.202842.01515.549658.4735
100.5202-0.2418-0.02790.4881-0.01010.5723-0.0418-0.152-0.02920.07760.07930.02640.0243-0.037500.18250.0130.01540.190.01750.175627.09420.284571.762
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 33:83)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 84:128)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 129:186)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 187:229)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 230:582)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 33:83)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 84:125)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 126:228)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 229:367)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 368:582)

+
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