[English] 日本語
Yorodumi
- PDB-6bl3: Crystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bl3
TitleCrystal Complex of Cyclooxygenase-2 with indomethacin-butyldiamine-dansyl conjugate
ComponentsProstaglandin G/H synthase 2
KeywordsOXIDOREDUCTASE/INHIBITOR / cyclooxygenase-2 / fluorescent inhibitor complex / OXIDOREDUCTASE-INHIBITOR complex
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-L7M / Prostaglandin G/H synthase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.217 Å
AuthorsXu, S. / Uddin, M.J. / Banerjee, S. / Marnett, L.J.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Fluorescent indomethacin-dansyl conjugates utilize the membrane-binding domain of cyclooxygenase-2 to block the opening to the active site.
Authors: Xu, S. / Uddin, M.J. / Banerjee, S. / Duggan, K. / Musee, J. / Kiefer, J.R. / Ghebreselasie, K. / Rouzer, C.A. / Marnett, L.J.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.2May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 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 / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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.d_res_low / _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 2.1Oct 4, 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 2.2Oct 16, 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
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,66330
Polymers269,3314
Non-polymers10,33226
Water15,421856
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,83215
Polymers134,6652
Non-polymers5,16613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-14 kcal/mol
Surface area41870 Å2
MethodPISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,83215
Polymers134,6652
Non-polymers5,16613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11310 Å2
ΔGint-17 kcal/mol
Surface area41890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.474, 121.776, 134.800
Angle α, β, γ (deg.)90.00, 123.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#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: 67332.711 Da / Num. of mol.: 4
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 , 3 types, 18 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.: 4
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: 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.: 8
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
#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.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 3 types, 864 molecules

#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-L7M / 2-[1-(4-chlorobenzene-1-carbonyl)-5-methoxy-2-methyl-1H-indol-3-yl]-N-[4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)butyl]acetamide


Mass: 661.210 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H37ClN4O5S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.7
Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM ...Details: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.217→103.3 Å / Num. obs: 141148 / % possible obs: 97.83 % / Observed criterion σ(F): 1.34 / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1535 / Rpim(I) all: 0.0977 / Rrim(I) all: 0.1826 / Net I/σ(I): 5.97
Reflection shellResolution: 2.217→2.296 Å / Rmerge(I) obs: 1.424 / Num. unique obs: 13090 / CC1/2: 0.458 / Rpim(I) all: 0.9065

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NT1

3nt1


Resolution: 2.217→112.436 Å / SU ML: 0.3 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 4220 3 %
Rwork0.2047 --
obs0.2054 140568 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.217→112.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17896 0 700 856 19452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319164
X-RAY DIFFRACTIONf_angle_d0.78326089
X-RAY DIFFRACTIONf_dihedral_angle_d17.14211315
X-RAY DIFFRACTIONf_chiral_restr0.0492753
X-RAY DIFFRACTIONf_plane_restr0.0053320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2168-2.2420.40391150.33783722X-RAY DIFFRACTION80
2.242-2.26840.32961320.31634394X-RAY DIFFRACTION95
2.2684-2.29610.31481500.28924531X-RAY DIFFRACTION98
2.2961-2.32510.31051440.27854544X-RAY DIFFRACTION98
2.3251-2.35570.3231290.27274561X-RAY DIFFRACTION99
2.3557-2.3880.30961520.26234600X-RAY DIFFRACTION99
2.388-2.42210.30971410.25374574X-RAY DIFFRACTION99
2.4221-2.45830.26781430.24884584X-RAY DIFFRACTION99
2.4583-2.49670.27731350.23734608X-RAY DIFFRACTION99
2.4967-2.53760.24231420.23024540X-RAY DIFFRACTION99
2.5376-2.58140.25891460.22994558X-RAY DIFFRACTION98
2.5814-2.62830.25011440.22854593X-RAY DIFFRACTION99
2.6283-2.67890.24381430.23284561X-RAY DIFFRACTION99
2.6789-2.73360.27151420.23424581X-RAY DIFFRACTION99
2.7336-2.7930.28121420.23554632X-RAY DIFFRACTION99
2.793-2.8580.27791390.23114604X-RAY DIFFRACTION99
2.858-2.92950.28521420.23094605X-RAY DIFFRACTION99
2.9295-3.00870.2721430.22674584X-RAY DIFFRACTION99
3.0087-3.09720.25991450.22514557X-RAY DIFFRACTION98
3.0972-3.19720.28231370.21974548X-RAY DIFFRACTION98
3.1972-3.31150.26831380.22154593X-RAY DIFFRACTION99
3.3115-3.44410.23771470.20424582X-RAY DIFFRACTION99
3.4441-3.60090.21431380.18554572X-RAY DIFFRACTION99
3.6009-3.79070.20271430.17594608X-RAY DIFFRACTION99
3.7907-4.02820.18451450.17254561X-RAY DIFFRACTION98
4.0282-4.33920.18351410.16364559X-RAY DIFFRACTION98
4.3392-4.77590.14331500.15554579X-RAY DIFFRACTION98
4.7759-5.4670.16261360.16454576X-RAY DIFFRACTION98
5.467-6.88770.24431350.20054598X-RAY DIFFRACTION98
6.8877-112.58120.20421410.19624639X-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)
10.58740.070.65820.9889-0.36171.8385-0.18240.01440.32060.2548-0.09280.1385-0.6470.06810.29060.50020.0124-0.09950.3119-0.04760.5164-42.7338-5.080623.5472
21.19090.2414-0.85270.5352-0.51122.69750.0191-0.09910.5910.175-0.04820.0681-0.5596-0.0880.10630.37050.0146-0.05640.3878-0.0360.4035-49.5776-16.611421.3087
30.77420.13960.37050.8501-0.04990.66320.00140.026-0.05830.0125-0.0459-0.16070.02880.09480.04250.25680.00340.01930.26740.02440.2026-40.1665-38.68920.1033
41.09910.06530.29290.5882-0.14250.8222-0.0164-0.17430.04150.1549-0.0229-0.0714-0.05410.03690.05570.2751-0.0046-0.01050.2551-0.0010.207-41.1983-30.038228.9457
51.0271-0.44050.52341.0582-0.77781.22170.0044-0.37370.00920.08660.13880.3452-0.2244-0.4381-0.16220.4030.07550.06950.5624-0.01260.427-80.9755-22.305114.7893
60.38060.01670.03941.9465-0.80910.5340.044-0.24310.26250.3665-0.05480.2291-0.1336-0.30210.02990.37130.00860.00440.4566-0.030.4182-68.5294-19.735810.0495
70.314-0.16810.36320.3570.02910.63920.1368-0.0859-0.148-0.0510.07070.2730.3369-0.3039-0.17720.3267-0.0726-0.03990.39060.11060.388-75.1009-39.58081.3829
80.67550.22350.12590.729-0.06860.61470.01370.15120.0561-0.1853-0.01350.02960.09350.0631-0.0030.3378-0.01170.00660.29620.05470.2527-57.2998-23.4384-13.221
91.2163-0.15970.18751.25140.04721.4307-0.26670.4495-0.0856-0.56420.2288-0.1095-0.03470.2393-0.0090.3865-0.02550.03940.33280.02250.2749-51.7341-20.8768-18.4671
100.94920.2480.50580.8851-0.28590.9531-0.06680.00880.0967-0.14380.06510.1735-0.0381-0.1424-0.01790.27970.0127-0.0180.25580.0270.2812-68.9457-18.9319-7.5073
111.95840.2059-0.01330.9591-0.22280.69630.1419-0.1736-0.6681-0.1242-0.0613-0.30650.18880.1997-0.19590.47690.0508-0.10940.3399-0.08120.589142.0109-57.240961.8715
122.36450.3345-1.21170.5697-0.43111.4678-0.01110.2092-0.4703-0.0442-0.1303-0.26270.3010.001-0.14950.38290.0415-0.05390.361-0.04740.417138.267-45.685155.7528
130.89720.28960.23860.9063-0.14290.57710.0112-0.0449-0.00880.18-0.0371-0.1379-0.0730.0380.01520.2789-0.0076-0.03670.2648-0.01050.271739.1987-23.65165.2833
141.01430.15220.41720.7281-0.10130.84990.00720.0774-0.10090.1005-0.0319-0.2971-0.03650.1955-0.02290.266-0.0003-0.04190.2994-0.01110.357647.5756-32.273862.2471
151.59720.6137-0.24990.3566-0.00410.6435-0.18890.6223-0.1931-0.30030.0546-0.0124-0.01120.2690.04950.4341-0.0380.05550.6743-0.04410.344927.823-34.360325.373
160.507-0.39270.57151.3303-0.19690.91370.01430.1813-0.3712-0.23180.2195-0.44170.40010.29780.10190.55450.0668-0.01180.5462-0.17560.445317.4959-58.599535.4308
170.79960.36010.41670.42340.1860.3788-0.2220.35080.3764-0.16310.1114-0.00190.0070.06590.05640.3322-0.0609-0.00690.41160.09280.258416.1591-23.94137.2561
180.63630.06540.2520.5843-0.34790.78540.0058-0.0510.12430.0831-0.04130.089-0.0221-0.1024-0.06860.2873-0.01410.03690.2805-0.01290.26332.9317-38.9655.992
191.53-0.02610.10411.4589-0.22721.01610.0251-0.0954-0.02090.15270.11780.12650.045-0.3406-0.00570.2804-0.00840.04560.2475-0.00080.2565-0.9312-41.581962.5877
201.26810.20160.34070.8134-0.19080.5382-0.00170.2156-0.0894-0.09220.10180.0540.077-0.0154-0.02420.2744-0.00680.01040.279-0.040.23145.8834-43.365343.3151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 105A)
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 319 )
4X-RAY DIFFRACTION4chain 'A' and (resid 320 through 583 )
5X-RAY DIFFRACTION5chain 'B' and (resid 33 through 105A)
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 138 )
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 181 )
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 269 )
9X-RAY DIFFRACTION9chain 'B' and (resid 270 through 319 )
10X-RAY DIFFRACTION10chain 'B' and (resid 320 through 583 )
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 105A)
12X-RAY DIFFRACTION12chain 'C' and (resid 106 through 138 )
13X-RAY DIFFRACTION13chain 'C' and (resid 139 through 319 )
14X-RAY DIFFRACTION14chain 'C' and (resid 320 through 583 )
15X-RAY DIFFRACTION15chain 'D' and (resid 33 through 93 )
16X-RAY DIFFRACTION16chain 'D' and (resid 94 through 123 )
17X-RAY DIFFRACTION17chain 'D' and (resid 124 through 181 )
18X-RAY DIFFRACTION18chain 'D' and (resid 182 through 269 )
19X-RAY DIFFRACTION19chain 'D' and (resid 270 through 319 )
20X-RAY DIFFRACTION20chain 'D' and (resid 320 through 583 )

+
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