[English] 日本語
Yorodumi
- PDB-4ptg: Structure of a carboxamine compound (26) (2-{2-[(CYCLOPROPYLCARBO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ptg
TitleStructure of a carboxamine compound (26) (2-{2-[(CYCLOPROPYLCARBONYL)AMINO]PYRIDIN-4-YL}-4-METHOXYPYRIMIDINE-5-CARBOXAMIDE) to GSK3b
ComponentsGlycogen synthase kinase-3 beta
Keywordstransferase/transferase inhibitor / Serine/threonine kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...regulation of microtubule anchoring at centrosome / negative regulation of glycogen (starch) synthase activity / neuron projection organization / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / tau-protein kinase / CRMPs in Sema3A signaling / heart valve development / regulation of microtubule-based process / regulation of protein export from nucleus / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / negative regulation of protein localization to nucleus / negative regulation of TOR signaling / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / positive regulation of cell-matrix adhesion / regulation of axon extension / G protein-coupled dopamine receptor signaling pathway / negative regulation of phosphoprotein phosphatase activity / regulation of dendrite morphogenesis / establishment of cell polarity / regulation of axonogenesis / tau-protein kinase activity / glycogen metabolic process / ER overload response / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / NF-kappaB binding / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / presynaptic modulation of chemical synaptic transmission / negative regulation of insulin receptor signaling pathway / excitatory postsynaptic potential / positive regulation of protein export from nucleus / positive regulation of GTPase activity / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of protein-containing complex assembly / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / tau protein binding / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / Regulation of RUNX2 expression and activity / neuron projection development / positive regulation of neuron apoptotic process / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / positive regulation of protein binding / insulin receptor signaling pathway / negative regulation of neuron projection development / kinase activity
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2WG / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.361 Å
AuthorsLewis, H.A. / Sivaprakasam, P. / Kish, K. / Pokross, M. / Dubowchik, G.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of new acylaminopyridines as GSK-3 inhibitors by a structure guided in-depth exploration of chemical space around a pyrrolopyridinone core.
Authors: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / ...Authors: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / Park, H. / Nophsker, M. / Lippy, J.S. / Burton, C.R. / Langley, D.R. / Macor, J.E. / Dubowchik, G.M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Feb 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: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2164
Polymers98,5902
Non-polymers6272
Water3,279182
1
A: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6082
Polymers49,2951
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6082
Polymers49,2951
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.197, 83.372, 177.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 49294.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-2WG / 2-{2-[(cyclopropylcarbonyl)amino]pyridin-4-yl}-4-methoxypyrimidine-5-carboxamide


Mass: 313.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: GSK-3 was mixed with a 10-fold molar excess of compound (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 22% PEG 3350 and 3.0% w/v methanol. ...Details: GSK-3 was mixed with a 10-fold molar excess of compound (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 22% PEG 3350 and 3.0% w/v methanol. Crystals would nucleate within 1-3 days and continued to grow for an addition 5-10 days before harvesting., VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→94.7809 Å / Num. obs: 49754

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.361→47.803 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2521 5.08 %Random
Rwork0.171 ---
obs0.173 49645 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.361→47.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 46 182 5261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075211
X-RAY DIFFRACTIONf_angle_d0.9477127
X-RAY DIFFRACTIONf_dihedral_angle_d11.8481831
X-RAY DIFFRACTIONf_chiral_restr0.037831
X-RAY DIFFRACTIONf_plane_restr0.005911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3605-2.40590.34151400.23892557X-RAY DIFFRACTION98
2.4059-2.4550.25271740.21652530X-RAY DIFFRACTION98
2.455-2.50840.26251420.19792559X-RAY DIFFRACTION99
2.5084-2.56680.24431540.19292565X-RAY DIFFRACTION99
2.5668-2.63090.24981370.1882572X-RAY DIFFRACTION98
2.6309-2.70210.25391430.18372585X-RAY DIFFRACTION98
2.7021-2.78160.27981240.17982597X-RAY DIFFRACTION99
2.7816-2.87130.251270.18232605X-RAY DIFFRACTION99
2.8713-2.9740.25321510.19212575X-RAY DIFFRACTION99
2.974-3.0930.23641290.18412622X-RAY DIFFRACTION99
3.093-3.23370.24381370.18812599X-RAY DIFFRACTION99
3.2337-3.40420.21621310.18492632X-RAY DIFFRACTION99
3.4042-3.61740.22021450.18342622X-RAY DIFFRACTION99
3.6174-3.89660.23111340.16362632X-RAY DIFFRACTION99
3.8966-4.28850.16681320.14732663X-RAY DIFFRACTION99
4.2885-4.90850.18741300.13052682X-RAY DIFFRACTION99
4.9085-6.18210.1691270.16282711X-RAY DIFFRACTION99
6.1821-47.81320.17251640.17392816X-RAY DIFFRACTION99
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)
15.51340.96530.19316.0636-0.97733.7689-0.1311-0.0716-0.10180.6770.01440.70830.059-0.16970.18860.5658-0.10130.04930.2668-0.01680.555-7.3282-15.048141.5316
25.50960.5919-0.49462.3178-1.02133.3101-0.11010.4493-0.0054-0.18240.02990.07730.2717-0.14810.07380.4872-0.03350.01440.19530.02620.45690.5829-8.190434.9853
35.63984.3593.21633.60222.07043.13840.0347-0.2292-0.19590.0379-0.1513-0.05260.3333-0.03350.25870.55940.05940.05880.29370.0320.46552.9657-9.506143.5117
43.651.7147-0.86556.33580.73742.089-0.42480.22970.0305-0.41120.04040.5322-0.1806-0.24240.25960.4989-0.00830.05520.34480.0020.38010.7254-5.231236.0916
52.56022.2723-0.03684.0358-0.18424.1256-0.31020.12410.60520.24010.43240.6773-0.62270.1719-0.14240.55090.0553-0.01180.33730.09530.48119.814317.136736.7102
61.3809-0.2127-0.75071.7180.4473.1934-0.0598-0.0319-0.0444-0.149-0.0537-0.05740.2610.20270.13410.45170.04940.03030.29830.02630.345414.21230.406943.5113
72.24450.6388-1.48992.36021.8153.6966-0.0567-0.0603-0.1078-0.17690.0853-0.09380.22740.49-0.02120.49560.06560.01410.4210.05030.341424.9487-0.721234.301
82.8274-1.3245-1.60563.39551.3664.3030.24470.46070.1192-0.3764-0.12010.0198-0.8680.1375-0.21510.5283-0.02340.04180.51210.06010.423127.980510.331228.537
92.24052.64520.36318.889-1.58833.33540.0943-0.532-0.9652-1.0206-1.0406-1.55070.87170.30760.59450.57320.196-0.01661.05510.22060.737840.24331.893334.1503
105.84361.5975-0.56341.43881.32352.30160.3641-0.2720.0212-0.30960.9180.3748-0.087-0.5998-1.29491.2638-0.27780.28341.0614-0.04291.00239.157614.082331.4738
110.93322.23170.89495.84151.5985.01970.28310.0360.514-0.78030.0028-0.6289-1.40881.3461-0.4380.9053-0.185-0.02270.57780.04460.551426.960720.350641.6292
125.20292.19320.46098.59633.16174.0785-0.1495-1.10390.6808-1.04310.3518-0.0404-0.4730.5849-0.01510.4472-0.1325-0.09560.5998-0.01330.489627.868112.208446.0904
131.8773-0.5114-0.97713.18870.70334.58-0.2486-0.36250.10730.52280.1910.1826-0.15690.68440.03470.4643-0.0248-0.0350.36970.03970.401220.89348.430551.3446
143.08181.6081.83485.0374-3.34735.483-0.3062-0.5774-0.24081.3592-0.00950.59270.1976-0.37120.15840.56470.04130.03140.31530.03230.345810.92623.433957.4633
158.12682.848-2.07857.20770.10046.9321-0.5636-0.2097-0.6914-0.447-0.1024-0.79870.93250.23260.6050.78850.17290.0410.36560.04670.364921.195-6.979656.1249
165.6579-0.9704-1.68054.6895-1.31772.3565-0.5765-1.35780.56720.97020.3461-0.1694-0.28450.91420.25290.5215-0.0164-0.10620.72680.11450.313823.77630.417161.1433
178.2884-2.7548-1.46375.1629-0.14538.4704-0.5808-0.8830.98961.26570.52250.0621-0.84340.19330.23650.67610.1385-0.05880.69650.0160.334415.14785.805365.2965
185.3536-1.4854-1.69153.6492-0.10822.8189-0.17680.54860.7295-0.52590.2827-1.29330.37350.3910.13310.4673-0.22470.06780.4984-0.03490.679342.987726.26993.2544
199.45290.4931-0.29474.2124-0.16030.09770.65260.01621.16170.5049-0.14120.1974-0.84790.0106-0.10020.4066-0.07850.07680.541-0.09630.510731.2629.58159.4475
207.4170.17451.52139.338-4.53848.7053-0.0918-1.34270.3350.55290.0911-0.65390.23550.6803-0.25810.30990.08610.04740.69030.01040.47628.774522.670514.4041
216.6768-0.35072.75964.99161.43242.14750.2751-0.83610.4349-0.4768-0.0145-0.5545-0.67750.9144-0.0347-0.0156-0.04260.04470.75150.02840.441535.572622.710510.1669
225.88795.0261-1.56854.2743-1.44812.64890.55850.86460.1674-0.03250.84720.28980.02430.5466-1.03060.29210.06770.08330.7339-0.02760.639139.050511.57498.4178
235.62973.45612.33696.70852.93242.557-0.39510.22510.223-0.58720.5763-0.3467-0.56920.7746-0.28890.3294-0.06150.08880.6157-0.04510.40736.628417.4173.6489
245.27650.46390.19053.2970.35242.46050.3371-0.5320.58630.2909-0.35610.1139-0.14620.00430.05340.3243-0.03810.03550.42480.05050.280531.188321.149110.0353
252.54690.4905-2.08254.74361.6256.7450.28510.44020.61170.1959-0.32710.6560.3153-1.24530.05960.32660.07520.00060.5773-0.02930.55588.389612.08247.2037
261.2105-0.21790.82121.5491-0.17133.82470.0508-0.0109-0.0496-0.2556-0.1956-0.06980.24660.26840.11880.37250.09590.04020.472-0.00250.385824.88754.07821.3951
272.02090.77340.06952.6268-0.43186.6568-0.1347-0.03050.4312-0.0719-0.1796-0.0234-0.6146-0.08180.11580.28570.06670.01830.42860.0460.404720.577613.54162.2093
281.6639-1.05151.21134.314-0.49922.67510.0192-0.09760.0163-0.1766-0.3181-0.5819-0.3190.7212-0.08020.26540.13350.04420.71370.08330.442835.07764.477910.1947
292.0037-1.2321-0.09844.11871.09441.12810.1288-0.34750.4599-0.0849-0.0179-0.72410.55290.66450.01490.38840.2694-0.03590.74720.05650.395635.1058-2.889717.2072
301.85520.61230.54642.8291-0.5174.477-0.1129-0.141-0.17690.4865-0.0878-0.15730.63370.42940.08280.51290.08940.01290.44440.01950.422826.0483-4.72616.7656
311.747-0.38541.63672.802-0.50314.0628-0.12540.1725-0.3911-0.1074-0.13290.15840.5170.04720.1030.36240.04690.03750.3625-0.00780.315718.9533-0.87047.814
321.6538-0.29941.51511.5361-1.47634.9913-0.1856-0.1469-0.19650.6410.12340.12450.1469-0.5210.16890.45110.04750.02190.4586-0.01860.393812.7121-0.167217.4074
332.84810.27470.64682.86260.20475.5386-0.4102-0.4330.08360.37090.00340.66610.1863-0.69780.07080.5351-0.01630.0840.46020.00380.478914.2047-8.367419.21
346.71561.9255-0.89523.9081-0.56182.7838-0.8294-0.8088-0.6176-0.5040.13160.06431.04271.10180.63381.30430.32240.04180.59170.11260.773422.349-17.981815.38
356.0831-2.80180.27783.58140.83690.42580.9935-0.4926-1.61491.5575-0.73090.72681.2469-1.3311-0.03760.9258-0.2931-0.07190.9955-0.09380.63776.8027-10.89698.4357
365.59363.38240.26353.98440.28238.41490.1715-0.2323-1.2795-0.69770.08240.92150.9369-1.3128-0.04270.5248-0.141-0.05870.4855-0.07820.562310.2679-5.83641.2153
373.77390.15370.15081.86541.34584.22350.05310.6724-0.008-0.3981-0.21630.2240.3240.16950.21880.46230.11750.00570.4389-0.03340.351822.2033-0.4153-7.0205
382.93311.06230.4895.4462-3.42892.65550.0981.09310.2382-1.20371.10730.0655-0.3894-1.2615-1.18350.83390.1520.04550.9351-0.01120.397824.12572.8833-20.8184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 154 )
6X-RAY DIFFRACTION6chain 'A' and (resid 155 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 252 )
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 273 )
9X-RAY DIFFRACTION9chain 'A' and (resid 274 through 284 )
10X-RAY DIFFRACTION10chain 'A' and (resid 293 through 300 )
11X-RAY DIFFRACTION11chain 'A' and (resid 301 through 310 )
12X-RAY DIFFRACTION12chain 'A' and (resid 311 through 320 )
13X-RAY DIFFRACTION13chain 'A' and (resid 321 through 354 )
14X-RAY DIFFRACTION14chain 'A' and (resid 355 through 363 )
15X-RAY DIFFRACTION15chain 'A' and (resid 364 through 370 )
16X-RAY DIFFRACTION16chain 'A' and (resid 371 through 377 )
17X-RAY DIFFRACTION17chain 'A' and (resid 378 through 382 )
18X-RAY DIFFRACTION18chain 'B' and (resid 37 through 51 )
19X-RAY DIFFRACTION19chain 'B' and (resid 52 through 64 )
20X-RAY DIFFRACTION20chain 'B' and (resid 65 through 74 )
21X-RAY DIFFRACTION21chain 'B' and (resid 75 through 95 )
22X-RAY DIFFRACTION22chain 'B' and (resid 96 through 101 )
23X-RAY DIFFRACTION23chain 'B' and (resid 102 through 119 )
24X-RAY DIFFRACTION24chain 'B' and (resid 124 through 138 )
25X-RAY DIFFRACTION25chain 'B' and (resid 139 through 154 )
26X-RAY DIFFRACTION26chain 'B' and (resid 155 through 183 )
27X-RAY DIFFRACTION27chain 'B' and (resid 184 through 198 )
28X-RAY DIFFRACTION28chain 'B' and (resid 199 through 208 )
29X-RAY DIFFRACTION29chain 'B' and (resid 209 through 218 )
30X-RAY DIFFRACTION30chain 'B' and (resid 219 through 235 )
31X-RAY DIFFRACTION31chain 'B' and (resid 236 through 252 )
32X-RAY DIFFRACTION32chain 'B' and (resid 253 through 261 )
33X-RAY DIFFRACTION33chain 'B' and (resid 262 through 273 )
34X-RAY DIFFRACTION34chain 'B' and (resid 274 through 284 )
35X-RAY DIFFRACTION35chain 'B' and (resid 298 through 304 )
36X-RAY DIFFRACTION36chain 'B' and (resid 305 through 320 )
37X-RAY DIFFRACTION37chain 'B' and (resid 321 through 377 )
38X-RAY DIFFRACTION38chain 'B' and (resid 378 through 385 )

+
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://pdbjlvh1.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