[English] 日本語
Yorodumi
- PDB-6s1i: Crystal Structure of DYRK1A with small molecule inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s1i
TitleCrystal Structure of DYRK1A with small molecule inhibitor
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1ADYRK1A
KeywordsTRANSFERASE / Kinase / catalytic domain / phosphorylated
Function / homology
Function and homology information


histone H3T45 kinase activity / negative regulation of DNA methylation-dependent heterochromatin formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator ...histone H3T45 kinase activity / negative regulation of DNA methylation-dependent heterochromatin formation / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of mRNA splicing, via spliceosome / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / tau protein binding / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / peptidyl-tyrosine phosphorylation / protein self-association / nervous system development / actin binding / protein tyrosine kinase activity / peptidyl-serine phosphorylation / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / identical protein binding / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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. ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KR8 / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.38 Å
AuthorsSorrell, F.J. / Henderson, S.H. / Redondo, C. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Elkins, J.M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Mining Public Domain Data to Develop Selective DYRK1A Inhibitors.
Authors: Henderson, S.H. / Sorrell, F. / Bennett, J. / Hanley, M.T. / Robinson, S. / Hopkins Navratilova, I. / Elkins, J.M. / Ward, S.E.
History
DepositionJun 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 11, 2021Group: Advisory / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_residues / refine
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,17920
Polymers168,3264
Non-polymers2,85316
Water11,656647
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6744
Polymers42,0821
Non-polymers5933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9646
Polymers42,0821
Non-polymers8835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9646
Polymers42,0821
Non-polymers8835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5764
Polymers42,0821
Non-polymers4943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.317, 64.504, 147.586
Angle α, β, γ (deg.)90.000, 115.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 135 through 147 or (resid 148...
21(chain B and (resid 135 through 147 or (resid 148...
31(chain C and (resid 135 through 147 or (resid 148...
41(chain D and (resid 135 through 211 or (resid 212...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTYRTYR(chain A and (resid 135 through 147 or (resid 148...AA135 - 14711 - 23
12ILEILEVALVAL(chain A and (resid 135 through 147 or (resid 148...AA148 - 14924 - 25
13VALVALLYSLYS(chain A and (resid 135 through 147 or (resid 148...AA135 - 48111 - 357
14VALVALLYSLYS(chain A and (resid 135 through 147 or (resid 148...AA135 - 48111 - 357
15VALVALLYSLYS(chain A and (resid 135 through 147 or (resid 148...AA135 - 48111 - 357
16VALVALLYSLYS(chain A and (resid 135 through 147 or (resid 148...AA135 - 48111 - 357
21VALVALTYRTYR(chain B and (resid 135 through 147 or (resid 148...BB135 - 14711 - 23
22ILEILEVALVAL(chain B and (resid 135 through 147 or (resid 148...BB148 - 14924 - 25
23VALVALLYSLYS(chain B and (resid 135 through 147 or (resid 148...BB135 - 48111 - 357
24VALVALLYSLYS(chain B and (resid 135 through 147 or (resid 148...BB135 - 48111 - 357
25VALVALLYSLYS(chain B and (resid 135 through 147 or (resid 148...BB135 - 48111 - 357
26VALVALLYSLYS(chain B and (resid 135 through 147 or (resid 148...BB135 - 48111 - 357
31VALVALTYRTYR(chain C and (resid 135 through 147 or (resid 148...CC135 - 14711 - 23
32ILEILEVALVAL(chain C and (resid 135 through 147 or (resid 148...CC148 - 14924 - 25
33VALVALLYSLYS(chain C and (resid 135 through 147 or (resid 148...CC135 - 48111 - 357
34VALVALLYSLYS(chain C and (resid 135 through 147 or (resid 148...CC135 - 48111 - 357
35VALVALLYSLYS(chain C and (resid 135 through 147 or (resid 148...CC135 - 48111 - 357
36VALVALLYSLYS(chain C and (resid 135 through 147 or (resid 148...CC135 - 48111 - 357
41VALVALASNASN(chain D and (resid 135 through 211 or (resid 212...DD135 - 21111 - 87
42LYSLYSLYSLYS(chain D and (resid 135 through 211 or (resid 212...DD21288
43VALVALLYSLYS(chain D and (resid 135 through 211 or (resid 212...DD135 - 48111 - 357
44VALVALLYSLYS(chain D and (resid 135 through 211 or (resid 212...DD135 - 48111 - 357
45VALVALLYSLYS(chain D and (resid 135 through 211 or (resid 212...DD135 - 48111 - 357
46VALVALLYSLYS(chain D and (resid 135 through 211 or (resid 212...DD135 - 48111 - 357

-
Components

#1: Protein
Dual specificity tyrosine-phosphorylation-regulated kinase 1A / DYRK1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / hMNB


Mass: 42081.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13627, dual-specificity kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-KR8 / ~{N}-methyl-~{N}-phenyl-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine


Mass: 302.333 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H14N6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 37% PEG400 -- 0.2M lithium sulfate -- 0.1M tris pH 8.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.38→110.03 Å / Num. obs: 83417 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 40.48 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.053 / Rrim(I) all: 0.099 / Net I/σ(I): 7.6 / Num. measured all: 274154 / Scaling rejects: 116
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.38-2.443.40.8682058560970.6310.5541.0331.5
10.64-110.033.10.074310610130.9810.0490.08917.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mq1
Resolution: 2.38→70.972 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 4184 5.1 %
Rwork0.2006 77916 -
obs0.202 82100 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.52 Å2 / Biso mean: 52.3464 Å2 / Biso min: 23.24 Å2
Refinement stepCycle: final / Resolution: 2.38→70.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11164 0 192 647 12003
Biso mean--61.12 47.63 -
Num. residues----1383
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4046X-RAY DIFFRACTION8.5TORSIONAL
12B4046X-RAY DIFFRACTION8.5TORSIONAL
13C4046X-RAY DIFFRACTION8.5TORSIONAL
14D4046X-RAY DIFFRACTION8.5TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3797-2.40670.39811280.35592434256294
2.4067-2.43510.39271320.34972537266996
2.4351-2.46480.35021390.33432519265896
2.4648-2.4960.36631240.31722513263796
2.496-2.52880.34391460.30982528267496
2.5288-2.56340.36531370.31792570270797
2.5634-2.60010.42251360.31662544268097
2.6001-2.63890.31811240.28932574269897
2.6389-2.68010.32411550.26812576273198
2.6801-2.72410.31691330.25442547268098
2.7241-2.7710.3061180.26152593271198
2.771-2.82140.31281520.25462575272798
2.8214-2.87570.28971530.2582565271898
2.8757-2.93440.31691640.25692596276099
2.9344-2.99820.27061540.22572544269899
2.9982-3.06790.23271540.22942625277999
3.0679-3.14470.22961430.21792582272599
3.1447-3.22970.25351400.22342664280499
3.2297-3.32470.23831470.21832569271699
3.3247-3.4320.25381410.20082635277699
3.432-3.55470.21051280.18122633276199
3.5547-3.6970.17681410.17322629277099
3.697-3.86530.20041550.16672600275599
3.8653-4.0690.1751310.15132664279599
4.069-4.32390.14641470.14722627277499
4.3239-4.65770.15711410.13222634277599
4.6577-5.12630.16251150.13872651276699
5.1263-5.86780.24141400.184126832823100
5.8678-7.39160.19511200.187327382858100
7.3916-71.00360.16651460.17722767291399
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)
13.62140.68140.47854.44860.25124.38260.2080.08750.01960.09220.0323-0.77020.11010.6454-0.27880.4660.03990.03550.4445-0.09820.4053-54.954516.807166.1114
21.03560.2957-0.04692.0880.82251.14030.0498-0.2008-0.02640.27050.058-0.16840.11560.0011-0.09410.43580.00130.00060.30020.03850.3225-63.99684.4517159.5472
33.51391.1626-2.27172.3757-0.96672.00060.1763-0.30131.07360.46250.02980.4896-0.7318-0.2518-0.3870.76860.06610.20140.3448-0.10110.9365-75.054920.3728153.2162
40.77460.27240.49131.6445-0.61752.06960.0146-0.0280.07020.1449-0.00250.0283-0.2225-0.1316-0.010.35790.02830.06320.27270.01740.3367-74.59689.3676142.2842
55.94573.04432.30786.08452.69758.1601-0.30020.90941.1015-0.9703-0.05630.2502-0.8888-0.4190.19970.51210.15610.10450.48250.10460.4624-83.47617.3254130.2058
65.59112.36740.99687.89526.86856.2070.05321.06112.0074-1.91690.3398-0.077-1.6837-0.7652-0.37140.6397-0.01520.04670.63320.23980.5485-70.299813.9434121.2103
70.43420.17520.27091.8502-0.4412.41260.1039-0.0868-0.16590.0504-0.05310.04610.1453-0.1602-0.05130.2655-0.03520.02150.2850.02060.3537-75.3122-5.1119142.1721
88.8156-1.6246-3.07337.31413.16995.5042-0.4269-0.2533-1.03340.790.20680.07291.0843-0.01520.38040.5566-0.02670.09330.40050.14620.4386-78.5554-11.1128153.2726
93.416-0.79890.59866.8014-0.7823.50680.0774-0.10970.43290.21910.1148-0.9235-0.31750.4637-0.15360.4831-0.0660.05620.3911-0.1230.4574-56.1041-24.4826174
102.9151-0.5899-1.92495.28730.97124.74730.1870.3635-0.0153-0.0952-0.16790.1424-0.229-0.53660.04970.5603-0.06650.10760.4209-0.05890.2855-76.0573-30.0804172.5896
111.7661-1.324-0.73492.06282.24963.39440.20850.09790.2852-0.08840.0338-0.3126-0.1902-0.0079-0.34840.5482-0.04550.13580.30270.01940.4381-67.4738-19.1998178.53
122.4381-1.0031-0.24854.01231.54111.9333-0.01220.02960.1703-0.3560.0389-0.16610.03840.06460.00180.49770.00030.06130.34930.0180.2774-79.214-19.7032182.4184
133.22822.25470.79017.16053.96442.30680.8306-0.5173-2.39950.33140.5511-1.47381.45880.7695-1.34130.61850.2387-0.00320.72490.01290.8639-76.7061-39.3791189.0176
141.4518-0.0205-0.43211.3751-0.24431.9284-0.0503-0.106-0.1018-0.08010.0699-0.09610.16070.17560.00980.42820.05680.05590.35760.00460.2725-80.5978-28.5902198.5621
152.70680.62160.1335.19873.23282.00630.0434-0.5852-0.35680.4259-0.02960.06710.6541-0.02450.16180.56330.05430.04740.52230.09630.2867-82.7903-32.8509212.7471
162.22390.93240.42984.34921.52493.105-0.11950.06720.2415-0.08550.10250.2424-0.2519-0.09950.03220.38730.0320.05110.2987-0.00040.2569-89.4802-14.512195.4935
172.98750.8190.55843.51330.14973.40680.3803-0.3811-0.53520.13-0.3009-0.59860.18790.6265-0.06980.5118-0.1365-0.10561.02660.1160.5165-114.4973-35.3433158.6039
184.14941.6726-0.89025.519-1.06378.4642-0.29080.40350.4531-0.52720.540.1241-0.4039-0.132-0.14750.6579-0.2068-0.10921.07030.1770.5209-128.0251-18.7072155.5981
191.8838-0.13521.2063.45181.27432.04040.1980.1448-0.3298-0.49180.1984-0.2421-0.39950.2938-0.2970.5862-0.1822-0.03220.92690.05190.4267-118.2999-27.51156.3486
201.0805-0.15240.71631.47570.141.7481-0.11610.28380.0107-0.04440.13540.012-0.057-0.2358-0.02960.5072-0.1553-0.00520.76240.13470.366-120.0547-14.5196169.0629
214.5683-2.46250.55191.4184-0.1950.1730.3023-0.7172-1.5976-1.26610.90692.18531.6711-2.3987-1.5490.8671-0.329-0.17431.2022-0.0320.8725-138.1039-25.6791170.578
221.34730.3783-0.10692.3673-0.80113.3437-0.13060.30570.0421-0.13850.20680.40010.0734-0.6697-0.07440.4193-0.10530.00230.7330.10750.4097-131.8883-18.7197183.4846
231.58213.1962-0.07032.02751.11491.8649-0.1518-0.8141-0.43721.65930.02640.8621-0.0539-0.98170.06330.5827-0.0960.1831.24310.16250.6434-142.31-20.5148198.5056
242.3084-0.37260.69232.5517-1.4325.0406-0.04070.31320.40060.05880.18660.2635-0.5896-0.3727-0.10830.47080.02010.06930.57760.10610.4291-125.3283-4.9695183.1109
253.9773-0.8317-0.28164.87471.36963.81720.57190.2858-1.2140.0214-0.16250.35280.8135-0.139-0.34830.66460.0044-0.3150.8206-0.07980.78-122.0358-20.1904116.7014
264.6964-1.95042.62072.4526-0.56712.30040.24850.9948-0.4458-0.6433-0.17020.35760.17390.36-0.0160.56040.0938-0.15460.7633-0.10750.4445-110.4354-10.6481113.7414
274.2005-1.00680.78952.84630.0651.96350.33180.3766-0.7246-0.3723-0.2660.31830.1821-0.0973-0.15360.377-0.0041-0.06260.6026-0.08990.4531-101.0328-16.9057126.1406
283.09851.5146-4.09533.5255-0.30046.47510.5621-0.26581.1178-0.2769-0.41531.2159-0.6377-0.5927-0.72350.30190.03610.05940.8670.07691.3777-111.15411.1221132.7242
292.0014-0.3951-0.26752.40470.22271.53140.1141-0.14280.00660.1264-0.15330.2681-0.0858-0.4520.03780.3637-0.04520.02410.60460.03530.3629-102.941-2.7999144.0181
303.6649-2.179-0.78322.04491.36021.9624-0.3989-0.7792-0.72170.41460.23330.37420.24550.42770.10430.4418-0.06730.02040.6540.20630.4766-93.912-16.5681149.6358
314.0058-2.09250.42772.71350.76121.40290.13420.2009-0.32320.2814-0.16070.02170.10150.0529-0.01740.3416-0.0644-0.0460.46760.04670.3975-88.4024-11.4811137.9909
328.90293.4186-3.63447.8562-1.05922.4922-0.02050.3003-0.4069-0.433-0.7256-0.56080.18681.22140.47130.45760.01270.04940.72420.05070.4214-84.4034-10.2109128.3255
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 135:216)A135 - 216
2X-RAY DIFFRACTION2(chain A and resid 217:313)A217 - 313
3X-RAY DIFFRACTION3(chain A and resid 314:322)A314 - 322
4X-RAY DIFFRACTION4(chain A and resid 323:389)A323 - 389
5X-RAY DIFFRACTION5(chain A and resid 390:408)A390 - 408
6X-RAY DIFFRACTION6(chain A and resid 409:414)A409 - 414
7X-RAY DIFFRACTION7(chain A and resid 415:474)A415 - 474
8X-RAY DIFFRACTION8(chain A and resid 475:481)A475 - 481
9X-RAY DIFFRACTION9(chain B and resid 135:197)B135 - 197
10X-RAY DIFFRACTION10(chain B and resid 198:217)B198 - 217
11X-RAY DIFFRACTION11(chain B and resid 218:255)B218 - 255
12X-RAY DIFFRACTION12(chain B and resid 256:313)B256 - 313
13X-RAY DIFFRACTION13(chain B and resid 314:322)B314 - 322
14X-RAY DIFFRACTION14(chain B and resid 323:391)B323 - 391
15X-RAY DIFFRACTION15(chain B and resid 392:422)B392 - 422
16X-RAY DIFFRACTION16(chain B and resid 423:481)B423 - 481
17X-RAY DIFFRACTION17(chain C and resid 135:201)C135 - 201
18X-RAY DIFFRACTION18(chain C and resid 202:219)C202 - 219
19X-RAY DIFFRACTION19(chain C and resid 220:243)C220 - 243
20X-RAY DIFFRACTION20(chain C and resid 244:313)C244 - 313
21X-RAY DIFFRACTION21(chain C and resid 314:322)C314 - 322
22X-RAY DIFFRACTION22(chain C and resid 323:395)C323 - 395
23X-RAY DIFFRACTION23(chain C and resid 396:411)C396 - 411
24X-RAY DIFFRACTION24(chain C and resid 412:481)C412 - 481
25X-RAY DIFFRACTION25(chain D and resid 135:196)D135 - 196
26X-RAY DIFFRACTION26(chain D and resid 197:237)D197 - 237
27X-RAY DIFFRACTION27(chain D and resid 238:313)D238 - 313
28X-RAY DIFFRACTION28(chain D and resid 314:321)D314 - 321
29X-RAY DIFFRACTION29(chain D and resid 322:412)D322 - 412
30X-RAY DIFFRACTION30(chain D and resid 413:438)D413 - 438
31X-RAY DIFFRACTION31(chain D and resid 439:469)D439 - 469
32X-RAY DIFFRACTION32(chain D and resid 470:481)D470 - 481

+
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