[English] 日本語
Yorodumi
- PDB-4ezl: Potent and Selective Inhibitors of PI3K-delta: Obtaining Isoform ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ezl
TitlePotent and Selective Inhibitors of PI3K-delta: Obtaining Isoform Selectivity from the Affinity Pocket and Tryptophan Shelf
ComponentsPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase p110 / p110-gamma / lipid kinase / cytoplasmic / 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-0SE / 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: 2.94 Å
AuthorsMurray, J.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Potent and selective inhibitors of PI3K-delta: obtaining isoform selectivity from the affinity pocket and tryptophan shelf
Authors: Sutherlin, D.P. / Baker, S. / Bisconte, A. / Blaney, P.M. / Brown, A. / Chan, B.K. / Chantry, D. / Castanedo, G. / DePledge, P. / Goldsmith, P. / Goldstein, D.M. / Hancox, T. / Kaur, J. / ...Authors: Sutherlin, D.P. / Baker, S. / Bisconte, A. / Blaney, P.M. / Brown, A. / Chan, B.K. / Chantry, D. / Castanedo, G. / DePledge, P. / Goldsmith, P. / Goldstein, D.M. / Hancox, T. / Kaur, J. / Knowles, D. / Kondru, R. / Lesnick, J. / Lucas, M.C. / Lewis, C. / Murray, J. / Nadin, A.J. / Nonomiya, J. / Pang, J. / Pegg, N. / Price, S. / Reif, K. / Safina, B.S. / Salphati, L. / Staben, S. / Seward, E.M. / Shuttleworth, S. / Sohal, S. / Sweeney, Z.K. / Ultsch, M. / Waszkowycz, B. / Wei, B.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)111,1642
Polymers110,6991
Non-polymers4651
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.331, 67.194, 106.558
Angle α, β, γ (deg.)90.00, 96.10, 90.00
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: 110699.023 Da / Num. of mol.: 1 / Fragment: UNP residues 144-1102 / Mutation: K802T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3CG / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P48736, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-0SE / 2-(1-{[2-(2-aminopyrimidin-5-yl)-4-(morpholin-4-yl)pyrido[3,2-d]pyrimidin-6-yl]methyl}piperidin-4-yl)propan-2-ol


Mass: 464.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N8O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
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

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2011
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.935→50 Å / Num. obs: 20407 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.935-3.113.70.475199.8
3.11-3.233.70.365199.9
3.23-3.383.70.26199.8
3.38-3.563.70.202199.6
3.56-3.783.70.138199.7
3.78-4.073.60.12199.1
4.07-4.483.50.089199.2
4.48-5.133.50.072199.1
5.13-6.463.50.068199.8
6.46-503.50.05199

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.93 Å31.14 Å
Translation2.93 Å31.14 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8X
Resolution: 2.94→31.14 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.74 / σ(F): 1.35 / Phase error: 31.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 1044 5.12 %
Rwork0.244 --
obs0.245 20402 94.9 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.23 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 102.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.827 Å2-0 Å20.6987 Å2
2--4.0965 Å20 Å2
3---4.6886 Å2
Refinement stepCycle: LAST / Resolution: 2.94→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6735 0 34 1 6770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086932
X-RAY DIFFRACTIONf_angle_d1.5319383
X-RAY DIFFRACTIONf_dihedral_angle_d13.6372572
X-RAY DIFFRACTIONf_chiral_restr0.0681056
X-RAY DIFFRACTIONf_plane_restr0.0071187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.935-3.08940.36641110.34821909X-RAY DIFFRACTION67
3.0894-3.28280.3751500.33022897X-RAY DIFFRACTION100
3.2828-3.53590.34411600.29652884X-RAY DIFFRACTION100
3.5359-3.89110.28021570.25442886X-RAY DIFFRACTION100
3.8911-4.45280.24521560.23062879X-RAY DIFFRACTION99
4.4528-5.60470.24711560.21662926X-RAY DIFFRACTION99
5.6047-31.14590.24451540.21912977X-RAY DIFFRACTION100
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)
10.1267-0.2759-0.47253.12331.60641.8289-0.27850.7004-0.6852-0.5578-0.22450.61421.0089-0.77050.26970.7016-0.0259-0.06721.1187-0.37770.731227.2979-37.6794.4442
21.132-0.2571-0.59850.44330.34680.43710.24820.5113-0.2314-0.52140.1274-0.2329-0.21010.3719-0.36370.90880.0504-0.19790.719-0.38280.677242.8478-32.66586.7393
30.53160.2628-0.05591.0905-0.10720.46470.15380.3235-0.95930.45340.29330.07850.60930.28091.13520.91990.5204-0.309-0.3634-0.54021.277336.7844-41.62417.8436
41.5309-0.8692-0.57160.50870.52172.32680.1526-0.3413-0.37340.30850.2097-0.02190.6247-0.62820.0810.9149-0.05970.01350.76240.41541.090518.2939-34.529133.2758
51.1651-0.5680.1541.31741.04642.67730.0455-0.42240.3080.46160.0182-0.28-0.0763-0.1271-0.04011.9595-0.04070.50821.8225-0.03061.037813.7318-18.049249.1572
62.35970.10550.5592.3017-0.2861.633-0.0989-1.1758-0.11630.2875-0.31650.51720.5967-0.50720.15110.83810.10510.45711.70840.5411.086-0.2078-30.338840.9243
73.6063-0.00290.77780.38770.96492.5857-0.1917-0.1181-0.972-0.0251-0.19670.38040.8005-0.11180.11921.0164-0.3845-0.0381.1321-0.0151.30582.1114-37.031630.7728
80.82011.21591.30331.79061.92052.06040.7462-0.37170.20940.27720.2850.2970.4147-0.25090.14730.9726-0.33490.34571.35290.33070.932610.3742-31.021132.3144
92.1205-1.181.2974.3-1.1743.4349-0.13220.0258-0.582-0.52570.3577-0.1097-0.29570.1468-0.20820.75860.33070.18581.31960.351.130512.633-23.747239.2442
106.51476.12015.6645.76595.36155.0045-0.07510.21460.5683-0.38650.37660.4284-0.7193-0.5109-0.11531.44540.17910.44161.0110.29141.43814.9442-18.461536.5248
110.3675-0.9922-0.27842.77520.63580.3484-0.26390.1281-0.4706-0.4144-0.09670.14620.7751-0.64640.380.4867-0.13540.04311.3563-0.02871.28774.0298-35.475526.7486
120.34290.4085-0.14840.5945-0.47440.9241-0.17880.4544-0.3167-0.5537-0.0781-0.04290.146-0.46320.29180.94550.0168-0.35460.7458-0.24351.169718.7058-43.400815.8641
131.5619-0.03680.68194.4191-1.33262.8189-0.06770.1363-0.6511-0.58520.19440.08450.11750.6533-0.09430.33960.24660.08261.3868-0.12960.521567.9879-30.753312.9507
140.04410.01340.03360.03530.06370.1291-0.91040.58771.5975-0.7571-0.81860.5804-1.38940.24220.87551.321-0.4986-0.21941.2740.20241.086360.7371-8.21010.6569
151.40830.3132-1.11852.6742-1.62683.85120.32441.04370.1257-0.2605-0.22680.1137-0.1731.3854-0.06770.5417-0.0079-0.01991.17080.02980.460665.3984-23.946616.3818
164.6509-0.1660.03630.95291.00862.8407-0.40560.11120.83710.2203-0.30030.12650.03320.43750.40780.5228-0.2051-0.0650.8051-0.19530.495759.9271-19.119514.9847
172.19530.69960.19040.69840.91111.50780.2573-0.0062-0.0612-0.6384-0.1373-0.0962-0.9140.06990.00220.72750.20630.1330.8182-0.10830.561255.6978-23.016814.4475
185.6439-0.835-2.82625.37080.6462.14690.0913-0.1972-0.24620.2987-0.15380.19710.2308-0.4069-0.00410.9120.48870.12220.52970.02480.866652.8194-41.267918.3223
192.00251.09960.18290.8814-0.84233.2541-0.12730.5258-0.5913-0.1589-0.46220.13220.52430.1730.06330.78120.1501-0.09791.2612-0.27030.380658.2056-31.42748.8664
202.29940.54942.22990.35430.20384.4481-0.0356-0.27430.66370.0907-0.26760.5073-1.0983-0.0620.01870.83860.0420.31140.7271-0.17440.757150.0798-13.591411.3443
215.9725-1.32940.71683.93510.9882.10580.1138-0.41331.02180.45410.0186-0.5323-1.18350.7472-0.12890.77880.0377-0.00030.6307-0.15610.748349.123-17.710320.9676
223.33280.3256-1.03165.59092.11941.2056-0.05430.0427-0.3524-0.03560.46880.01260.4315-0.0217-0.08030.50320.3252-0.02430.8837-0.13770.361548.7376-25.046111.7039
238.02885.2917-4.79799.151-1.66528.3332-0.12960.3428-0.1421-0.3665-0.14170.1946-0.055-0.09550.02980.7559-0.13470.00821.059-0.12980.861147.9244-20.7830.595
241.62490.2643-1.66863.45680.76122.026-0.02010.38730.2149-0.1765-0.51960.23030.1294-0.32230.11980.2652-0.02890.28421.2651-0.28940.633757.4653-21.43914.5311
251.73760.4226-0.63992.294-1.83494.126-0.1161-0.0666-0.24440.02880.0092-0.3350.5120.59040.1990.86630.38680.59811.3305-0.29820.674165.3855-34.290510.8435
262.8109-0.03091.22473.63810.15725.2034-0.3613-1.2247-0.7473-0.1199-0.1591-0.4652-0.419-0.15670.22460.49720.07550.18840.85030.0040.646357.3736-25.395255.0992
274.46170.1515-1.01143.2338-0.19863.43140.22040.30140.90740.4868-0.0004-0.1690.2353-0.1165-0.34880.69250.0510.00320.9494-0.15710.463656.6869-25.304445.4524
283.75710.4054-1.39612.7156-0.38683.8853-0.040.1267-0.4156-0.121-0.1674-0.73040.12540.36750.21290.31790.1173-0.09580.55150.1290.336956.2351-32.818538.5998
292.28470.6045-1.05831.07720.18423.5229-0.2716-0.666-0.76310.3921-0.0862-0.24480.73630.24790.0740.49610.007-0.04240.46240.14630.569644.3365-30.544439.4884
305.32882.62220.16812.1711-1.59093.22230.2674-0.4687-0.8830.18210.07120.5560.3243-0.1608-0.15960.5390.0732-0.14960.4820.23570.783439.9707-34.092435.277
313.2346-0.11590.76731.78090.02451.59980.21980.1593-0.49110.1342-0.11280.46060.18930.0004-0.13490.33950.0149-0.02890.2043-0.05970.399833.4241-29.04422.2595
322.9999-0.8168-1.0154.4895-1.64732.7280.0830.9655-0.6157-0.914-0.28020.49870.0193-0.9350.02110.41080.0397-0.09660.8006-0.10370.385520.9929-19.49078.812
332.81080.82270.14133.5452-1.02292.49370.10820.59720.3156-0.28560.04090.8302-0.1634-0.495-0.11350.6220.1734-0.01070.67250.05750.716513.594-12.369212.6781
342.033-0.50460.22561.77610.37871.0065-0.7366-0.13320.64090.6759-0.01930.3778-0.9486-0.73340.29540.98130.5508-0.10810.3522-0.18170.619321.0195-3.63231.8544
353.3533-0.4793-1.51071.67570.14692.5906-0.1745-0.42910.7710.4452-0.34420.2286-0.5287-0.3205-0.28431.97310.5647-0.37220.6076-0.53181.331725.04018.156741.1776
361.3159-0.615-0.98992.27010.96580.8688-0.4166-0.7520.52260.758-0.0563-0.4911-0.8142-0.47730.17091.17680.3758-0.12890.7723-0.12140.364932.8114-9.50342.2107
373.74242.53732.83631.7751.8692.193-0.02840.58570.3221-0.31920.334-0.3397-0.24181.0054-0.03021.143-0.10250.18821.683-0.14790.907347.4587-9.881225.7781
381.3597-0.4806-0.17061.6295-0.77391.598-0.5179-0.39291.0643-0.6907-0.08230.6009-1.6226-0.43410.07831.42950.0491-0.73630.4308-0.35930.956836.17452.679638.7534
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 143:158 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 159:171 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 172:188 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 189:208 )
5X-RAY DIFFRACTION5(CHAIN A AND RESID 209:214 )
6X-RAY DIFFRACTION6(CHAIN A AND RESID 215:251 )
7X-RAY DIFFRACTION7(CHAIN A AND RESID 267:274 )
8X-RAY DIFFRACTION8(CHAIN A AND RESID 275:286 )
9X-RAY DIFFRACTION9(CHAIN A AND RESID 287:298 )
10X-RAY DIFFRACTION10(CHAIN A AND RESID 299:304 )
11X-RAY DIFFRACTION11(CHAIN A AND RESID 305:312 )
12X-RAY DIFFRACTION12(CHAIN A AND RESID 313:320 )
13X-RAY DIFFRACTION13(CHAIN A AND RESID 357:369 )
14X-RAY DIFFRACTION14(CHAIN A AND RESID 370:381 )
15X-RAY DIFFRACTION15(CHAIN A AND RESID 382:427 )
16X-RAY DIFFRACTION16(CHAIN A AND RESID 428:435 )
17X-RAY DIFFRACTION17(CHAIN A AND RESID 460:469 )
18X-RAY DIFFRACTION18(CHAIN A AND RESID 470:474 )
19X-RAY DIFFRACTION19(CHAIN A AND RESID 475:484 )
20X-RAY DIFFRACTION20(CHAIN A AND RESID 485:489 )
21X-RAY DIFFRACTION21(CHAIN A AND RESID 497:502 )
22X-RAY DIFFRACTION22(CHAIN A AND RESID 503:507 )
23X-RAY DIFFRACTION23(CHAIN A AND RESID 508:512 )
24X-RAY DIFFRACTION24(CHAIN A AND RESID 513:517 )
25X-RAY DIFFRACTION25(CHAIN A AND RESID 518:522 )
26X-RAY DIFFRACTION26(CHAIN A AND RESID 544:560 )
27X-RAY DIFFRACTION27(CHAIN A AND RESID 561:585 )
28X-RAY DIFFRACTION28(CHAIN A AND RESID 586:612 )
29X-RAY DIFFRACTION29(CHAIN A AND RESID 613:637 )
30X-RAY DIFFRACTION30(CHAIN A AND RESID 638:652 )
31X-RAY DIFFRACTION31(CHAIN A AND RESID 653:725 )
32X-RAY DIFFRACTION32(CHAIN A AND RESID 726:753 )
33X-RAY DIFFRACTION33(CHAIN A AND RESID 760:837 )
34X-RAY DIFFRACTION34(CHAIN A AND RESID 838:966 )
35X-RAY DIFFRACTION35(CHAIN A AND RESID 981:1003 )
36X-RAY DIFFRACTION36(CHAIN A AND RESID 1004:1038 )
37X-RAY DIFFRACTION37(CHAIN A AND RESID 1039:1045 )
38X-RAY DIFFRACTION38(CHAIN A AND RESID 1046:1093 )

+
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