[English] 日本語
Yorodumi
- PDB-4j6i: Discovery of thiazolobenzoxepin PI3-kinase inhibitors that spare ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j6i
TitleDiscovery of thiazolobenzoxepin PI3-kinase inhibitors that spare the PI3-kinase beta isoform
ComponentsPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
KeywordsTransferase/Transferase Inhibitor / beta-sparing / SBDD / catalytic subunit gamma / phosphorylation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / regulation of calcium ion transmembrane transport / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / T cell chemotaxis ...secretory granule localization / negative regulation of triglyceride catabolic process / natural killer cell chemotaxis / neutrophil extravasation / phosphatidylinositol-4-phosphate 3-kinase / regulation of calcium ion transmembrane transport / positive regulation of acute inflammatory response / respiratory burst involved in defense response / negative regulation of cardiac muscle contraction / T cell chemotaxis / negative regulation of fibroblast apoptotic process / phosphatidylinositol 3-kinase complex, class IB / sphingosine-1-phosphate receptor signaling pathway / dendritic cell chemotaxis / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / phosphatidylinositol 3-kinase complex, class IA / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / mast cell degranulation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / hepatocyte apoptotic process / positive regulation of Rac protein signal transduction / regulation of cell adhesion mediated by integrin / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / regulation of angiogenesis / T cell proliferation / cellular response to cAMP / GPVI-mediated activation cascade / T cell activation / ephrin receptor binding / neutrophil chemotaxis / positive regulation of endothelial cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cytokine production / positive regulation of MAP kinase activity / platelet aggregation / endocytosis / G beta:gamma signalling through PI3Kgamma / Signaling by CSF1 (M-CSF) in myeloid cells / kinase activity / positive regulation of cytosolic calcium ion concentration / angiogenesis / adaptive immune response / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / protein kinase activity / immune response / inflammatory response / G protein-coupled receptor signaling pathway / phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / C2 domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. ...PIK3 catalytic subunit gamma, adaptor-binding domain / PIK3 catalytic subunit gamma adaptor-binding domain / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase, accessory domain (PIK) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 / C2 domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ubiquitin-like (UB roll) / Alpha Horseshoe / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1JV / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMurray, J.M. / Rouge, L. / Wu, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Discovery of thiazolobenzoxepin PI3-kinase inhibitors that spare the PI3-kinase beta isoform.
Authors: Staben, S.T. / Ndubaku, C. / Blaquiere, N. / Belvin, M. / Bull, R.J. / Dudley, D. / Edgar, K. / Gray, D. / Heald, R. / Heffron, T.P. / Jones, G.E. / Jones, M. / Kolesnikov, A. / Lee, L. / ...Authors: Staben, S.T. / Ndubaku, C. / Blaquiere, N. / Belvin, M. / Bull, R.J. / Dudley, D. / Edgar, K. / Gray, D. / Heald, R. / Heffron, T.P. / Jones, G.E. / Jones, M. / Kolesnikov, A. / Lee, L. / Lesnick, J. / Lewis, C. / Murray, J. / McLean, N.J. / Nonomiya, J. / Olivero, A.G. / Ord, R. / Pang, J. / Price, S. / Prior, W.W. / Rouge, L. / Salphati, L. / Sampath, D. / Wallin, J. / Wang, L. / Wei, B. / Weismann, C. / Wu, P.
History
DepositionFeb 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2182
Polymers110,7271
Non-polymers4911
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.671, 67.161, 106.655
Angle α, β, γ (deg.)90.000, 95.430, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform / PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / ...PI3-kinase subunit gamma / PI3K-gamma / PI3Kgamma / PtdIns-3-kinase subunit gamma / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit gamma / PtdIns-3-kinase subunit p110-gamma / p110gamma / Phosphoinositide-3-kinase catalytic gamma polypeptide / Serine/threonine protein kinase PIK3CG / p120-PI3K


Mass: 110727.102 Da / Num. of mol.: 1 / Fragment: UNP residues 144-1102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p110 gamma, PIK3CG / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P48736, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1JV / 2-methyl-1-(4-{2-[1-(2,2,2-trifluoroethyl)-1H-1,2,4-triazol-5-yl]-4,5-dihydro[1]benzoxepino[5,4-d][1,3]thiazol-8-yl}-1H-pyrazol-1-yl)propan-2-ol


Mass: 490.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21F3N6O2S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, 0.2M NH4SO4, 0.1M Tris-HCl 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2009
RadiationMonochromator: Side scattering I-beam bent single crystal / Protocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.87→50 Å / Num. obs: 22879 / % possible obs: 97.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 83 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.034 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.87-2.972.70.44618901.036181.6
2.97-3.093.10.39222001.083194.4
3.09-3.233.50.30223191.047199.6
3.23-3.43.70.19823321.014199.9
3.4-3.623.80.12323380.995199.9
3.62-3.893.80.08123231.001199.9
3.89-4.293.80.05523411.045199.9
4.29-4.913.80.04423541.041100
4.91-6.183.70.05123621.03199.8
6.18-503.60.02424201.063199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8_1068refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→19.85 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 1115 5.01 %
Rwork0.2053 --
obs0.2077 22244 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.37 Å2 / Biso mean: 94.9072 Å2 / Biso min: 34.99 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 34 0 6783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136966
X-RAY DIFFRACTIONf_angle_d1.9829432
X-RAY DIFFRACTIONf_chiral_restr0.0921056
X-RAY DIFFRACTIONf_plane_restr0.0121195
X-RAY DIFFRACTIONf_dihedral_angle_d15.3982589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.03160.31551040.26592391249589
3.0316-3.19080.33311540.26572598275298
3.1908-3.38980.31511170.242826742791100
3.3898-3.650.27431540.216526652819100
3.65-4.01460.29031410.208326662807100
4.0146-4.58920.22741550.186526792834100
4.5892-5.75850.26471460.197726962842100
5.7585-19.850.19721440.189927602904100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0053-0.1197-0.3051.49-2.08522.9741-0.19571.18-1.4068-1.1089-0.34890.27811.0734-0.30410.37280.8470.0537-0.19691.0842-0.47761.136228.673528.9684.5896
20.94910.3918-1.13620.9623-0.59051.383-0.5480.4182-0.657-0.5069-0.2947-0.37030.23970.21750.24940.9704-0.005-0.00481.2032-0.48890.858244.29134.29256.6338
31.13280.8313-0.51190.8513-0.66230.5746-0.28560.594-0.88180.0708-0.28651.08250.57810.03270.06260.70980.26170.0836-0.7253-0.90861.21138.505624.97417.4798
42.9037-0.49930.25771.2966-0.33033.94770.0257-0.2198-0.7994-0.0097-0.0960.14120.6333-0.6417-0.04480.561-0.0933-0.09220.630.14521.153320.091731.34333.3347
55.87840.91590.76620.6996-0.53760.89250.0149-0.78080.36360.6738-0.0922-0.1135-0.3087-0.21070.16261.91170.27940.22271.82680.06691.184415.586247.923249.2835
62.8007-0.32291.07952.1987-0.68332.5529-0.0162-1.42840.0447-0.1305-0.20520.46910.2782-0.9950.22870.5624-0.01130.1221.60680.37331.30881.908335.699341.3965
73.09430.01130.49780.58411.2042.521-0.0783-0.0621-1.61250.0501-0.55610.57720.69940.01720.57630.848-0.16380.08631.0317-0.08381.32174.001328.329331.3069
82.8661-0.16621.18772.7218-1.88366.57670.8743-0.2465-0.52470.00950.17510.0010.2782-0.2678-0.60080.882-0.08790.25110.7420.08930.849912.076434.911332.601
93.7848-0.67630.60323.25341.75693.4772-0.35170.1745-0.1989-0.2194-0.0769-0.4981-0.7437-0.1870.17330.98860.04370.28190.95250.06350.671714.295742.065239.5503
103.43780.13270.89120.0714-0.08180.42020.1152-0.2058-0.0264-0.00480.08060.8627-1.0234-0.3198-0.33050.82610.27110.24491.3554-0.06591.39216.786247.316636.9395
110.94111.29470.34721.78190.46640.1522-0.54030.19540.2011-0.2561-0.03150.61240.2703-1.09260.47350.543-0.12770.03031.2322-0.13361.35945.892530.063626.9374
122.11550.33891.38763.3789-1.78912.1297-0.38620.4381-0.4534-1.67760.4694-0.41811.07320.4618-0.01181.1619-0.0570.03070.6425-0.39761.268420.338722.496715.9483
131.87430.8426-0.71884.4904-1.50654.4071-0.3496-0.0288-0.5581-0.74790.3771-0.57150.83060.54910.19390.67320.20870.04481.2978-0.09770.621269.472436.648312.6487
140.0610.07360.06980.09930.07210.0623-0.2919-0.35581.5131-0.9536-0.36710.692-0.2158-0.05650.62411.2002-0.12530.081.33650.21161.353561.366259.26352.3007
151.82210.3614-0.85722.0429-0.94381.91290.15730.1893-0.2649-0.0724-0.174-0.1501-0.15470.48420.01240.4931-0.0302-0.04630.9311-0.15490.616766.884943.15516.217
162.52230.4258-1.04510.3011-1.07533.7434-0.32140.11890.62380.0566-0.3373-0.3426-0.82710.4530.44940.6005-0.1425-0.0620.8192-0.04160.593361.261247.98514.9897
174.55860.47350.00730.7711.28462.2323-0.17230.7035-0.3878-0.4248-0.060.1782-0.4716-0.22790.25860.72310.143-0.00860.6015-0.03060.410657.132344.060314.4501
182.292-1.0483-0.60191.24350.05560.22150.15040.1638-0.07080.0158-0.04060.0950.1473-0.40140.08290.83750.158300.519-0.24451.015154.613625.665217.924
190.99960.849-0.29970.785-0.60562.3640.0730.8425-0.8509-0.8132-0.1414-0.01120.62130.28290.08330.6590.18380.040.9516-0.30680.594459.645935.69958.662
204.77651.55340.96221.80733.09556.2410.7850.121.0844-0.24360.04820.3136-0.2426-0.2242-0.44050.8602-0.17030.24960.9328-0.11170.751251.147853.226411.6376
215.2574-0.8396-2.22012.9198-1.66144.2103-0.4674-0.07660.70480.125-0.5256-0.0084-0.95780.77910.8030.6899-0.2027-0.18370.7733-0.11880.691350.509949.161520.8611
221.6342-0.1447-0.29624.90320.51030.0996-0.15960.5199-0.257-0.20830.4144-0.34330.41980.1858-0.11360.43050.20020.03540.8168-0.20820.407550.259342.005711.6702
230.82490.8682-1.15230.9353-1.24261.6377-0.01360.36680.0349-0.59980.1333-0.3169-0.33610.2713-0.10170.9407-0.09480.07321.65750.00470.647149.388646.49540.4935
244.21382.09860.39184.090.91885.8400.87520.2631-0.63260.41540.23130.0662-0.2064-0.31020.6757-0.12520.08030.8990.02240.673558.840145.78094.6711
250.96810.9164-0.25411.0504-1.06664.0210.3315-0.0728-0.27560.3036-0.041-0.52930.64010.6338-0.29090.9130.29920.19541.1856-0.11670.89466.866432.75210.4962
268.3323-4.05043.92033.8255-3.43598.9182-0.1242-1.1812-0.10590.97360.2195-0.7733-0.20880.63770.23690.75840.1792-0.21560.93020.03180.652658.65743.035554.8045
274.6517-1.60840.11182.46580.39673.1634-0.79520.15690.37380.17570.8361-0.29810.5967-0.3714-0.07950.6436-0.0445-0.06171.07550.01740.642958.351241.337145.2701
283.9288-0.1552-1.0352.97990.44863.3254-0.2799-0.2495-0.481-0.04970.0088-0.50160.53570.43470.22170.49090.0132-0.07790.62920.08340.581557.976833.743638.3253
292.1056-0.1735-0.50530.65340.30611.43760.0772-0.7237-0.53960.90310.12110.29910.12320.0086-0.1880.7725-0.06110.03340.54940.16440.601646.08135.912939.2907
305.95131.1483-0.14292.3509-1.09822.69580.207-0.4225-0.42930.57110.09760.65970.2941-0.2878-0.33710.65020.06770.01160.53840.17380.676441.77232.308635.1306
312.989-0.45880.73271.9338-0.372.22420.14570.3358-0.7241-0.054-0.07930.19370.0872-0.0595-0.06150.4026-0.0271-0.01750.3154-0.11580.470834.898537.371722.1667
322.8973-0.3008-0.07867.2106-1.94764.10370.08891.6109-0.0747-0.6678-0.12760.2922-0.0021-1.203-0.1130.50150.149-0.0531.0319-0.01060.559821.974346.78398.8733
332.80050.1374-0.55462.3269-0.72412.70290.16690.82230.1818-0.4172-0.11710.6454-0.3529-0.5914-0.0010.73390.2361-0.09640.8870.06240.686414.469653.609112.8232
343.498-0.52460.62362.161-0.13672.3613-0.1217-0.29230.95630.7991-0.13620.5929-0.5861-0.40610.12170.82990.0850.14170.4787-0.17230.795322.553562.613932.2646
351.2302-0.68251.03381.3264-1.28641.7922-0.1249-1.04811.1840.2238-0.3708-0.2653-1.2124-0.31630.31761.6763-0.0151-0.00770.787-0.46771.257426.629774.331841.5182
361.92010.23930.24031.03350.59240.4287-0.1486-0.78890.39621.29550.111-0.0847-0.2475-0.2708-0.19051.19440.1006-0.00220.7619-0.17910.494334.511856.725642.422
370.08760.05410.02310.02870.0130.00580.13560.01920.24280.5784-0.0076-0.4576-0.04810.961-0.21541.4316-0.49860.13381.1783-0.16781.042548.326156.848525.5456
382.9207-1.642-0.54063.6855-0.71452.0374-0.3979-0.7421.80091.036-0.1546-0.2684-1.17360.25590.29141.2919-0.0507-0.1820.7614-0.39341.139338.019768.911939.4507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 143:158 )A143 - 158
2X-RAY DIFFRACTION2( CHAIN A AND RESID 159:171 )A159 - 171
3X-RAY DIFFRACTION3( CHAIN A AND RESID 172:188 )A172 - 188
4X-RAY DIFFRACTION4( CHAIN A AND RESID 189:208 )A189 - 208
5X-RAY DIFFRACTION5( CHAIN A AND RESID 209:214 )A209 - 214
6X-RAY DIFFRACTION6( CHAIN A AND RESID 215:250 )A215 - 250
7X-RAY DIFFRACTION7( CHAIN A AND RESID 267:274 )A267 - 274
8X-RAY DIFFRACTION8( CHAIN A AND RESID 275:286 )A275 - 286
9X-RAY DIFFRACTION9( CHAIN A AND RESID 287:298 )A287 - 298
10X-RAY DIFFRACTION10( CHAIN A AND RESID 299:304 )A299 - 304
11X-RAY DIFFRACTION11( CHAIN A AND RESID 305:312 )A305 - 312
12X-RAY DIFFRACTION12( CHAIN A AND RESID 313:320 )A313 - 320
13X-RAY DIFFRACTION13( CHAIN A AND RESID 357:369 )A357 - 369
14X-RAY DIFFRACTION14( CHAIN A AND RESID 370:381 )A370 - 381
15X-RAY DIFFRACTION15( CHAIN A AND RESID 382:427 )A382 - 427
16X-RAY DIFFRACTION16( CHAIN A AND RESID 428:435 )A428 - 435
17X-RAY DIFFRACTION17( CHAIN A AND RESID 460:469 )A460 - 469
18X-RAY DIFFRACTION18( CHAIN A AND RESID 470:474 )A470 - 474
19X-RAY DIFFRACTION19( CHAIN A AND RESID 475:484 )A475 - 484
20X-RAY DIFFRACTION20( CHAIN A AND RESID 485:489 )A485 - 489
21X-RAY DIFFRACTION21( CHAIN A AND RESID 497:502 )A497 - 502
22X-RAY DIFFRACTION22( CHAIN A AND RESID 503:507 )A503 - 507
23X-RAY DIFFRACTION23( CHAIN A AND RESID 508:512 )A508 - 512
24X-RAY DIFFRACTION24( CHAIN A AND RESID 513:517 )A513 - 517
25X-RAY DIFFRACTION25( CHAIN A AND RESID 518:522 )A518 - 522
26X-RAY DIFFRACTION26( CHAIN A AND RESID 546:560 )A546 - 560
27X-RAY DIFFRACTION27( CHAIN A AND RESID 561:585 )A561 - 585
28X-RAY DIFFRACTION28( CHAIN A AND RESID 586:612 )A586 - 612
29X-RAY DIFFRACTION29( CHAIN A AND RESID 613:637 )A613 - 637
30X-RAY DIFFRACTION30( CHAIN A AND RESID 638:652 )A638 - 652
31X-RAY DIFFRACTION31( CHAIN A AND RESID 653:725 )A653 - 725
32X-RAY DIFFRACTION32( CHAIN A AND RESID 726:753 )A726 - 753
33X-RAY DIFFRACTION33( CHAIN A AND RESID 760:837 )A760 - 837
34X-RAY DIFFRACTION34( CHAIN A AND RESID 838:967 )A838 - 967
35X-RAY DIFFRACTION35( CHAIN A AND RESID 981:1003 )A981 - 1003
36X-RAY DIFFRACTION36( CHAIN A AND RESID 1004:1038 )A1004 - 1038
37X-RAY DIFFRACTION37( CHAIN A AND RESID 1039:1045 )A1039 - 1045
38X-RAY DIFFRACTION38( CHAIN A AND RESID 1046:1087 )A1046 - 1087

+
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