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- PDB-7jxh: HER2 in complex with JBJ-08-178-01 -

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Basic information

Entry
Database: PDB / ID: 7jxh
TitleHER2 in complex with JBJ-08-178-01
ComponentsReceptor tyrosine-protein kinase erbB-2
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / HER2 / ErbB2 / kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / ErbB-3 class receptor binding / regulation of microtubule-based process / Sema4D induced cell migration and growth-cone collapse ...negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / semaphorin receptor complex / ErbB-3 class receptor binding / regulation of microtubule-based process / Sema4D induced cell migration and growth-cone collapse / motor neuron axon guidance / PLCG1 events in ERBB2 signaling / neurotransmitter receptor localization to postsynaptic specialization membrane / ERBB2-EGFR signaling pathway / positive regulation of Rho protein signal transduction / ERBB2 Activates PTK6 Signaling / neuromuscular junction development / positive regulation of transcription by RNA polymerase I / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / enzyme-linked receptor protein signaling pathway / ERBB2-ERBB3 signaling pathway / oligodendrocyte differentiation / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of protein targeting to membrane / regulation of angiogenesis / coreceptor activity / Schwann cell development / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / GRB2 events in ERBB2 signaling / transmembrane receptor protein tyrosine kinase activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / SHC1 events in ERBB2 signaling / positive regulation of cell adhesion / Downregulation of ERBB2:ERBB3 signaling / Constitutive Signaling by Overexpressed ERBB2 / neurogenesis / positive regulation of epithelial cell proliferation / basal plasma membrane / positive regulation of translation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / receptor protein-tyrosine kinase / neuron differentiation / cellular response to growth factor stimulus / receptor tyrosine kinase binding / Downregulation of ERBB2 signaling / peptidyl-tyrosine phosphorylation / ruffle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / protein tyrosine kinase activity / basolateral plasma membrane / positive regulation of MAPK cascade / early endosome / receptor complex / cell surface receptor signaling pathway / endosome membrane / intracellular signal transduction / protein heterodimerization activity / positive regulation of protein phosphorylation / protein phosphorylation / apical plasma membrane / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / plasma membrane
Similarity search - Function
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-VOY / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsBeyett, T.S. / Eck, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA201049-05 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1F32CA247198-01 United States
CitationJournal: Cancer Res. / Year: 2022
Title: A Novel HER2-Selective Kinase Inhibitor Is Effective in HER2 Mutant and Amplified Non-Small Cell Lung Cancer.
Authors: Son, J. / Jang, J. / Beyett, T.S. / Eum, Y. / Haikala, H.M. / Verano, A. / Lin, M. / Hatcher, J.M. / Kwiatkowski, N.P. / Eser, P.O. / Poitras, M.J. / Wang, S. / Xu, M. / Gokhale, P.C. / ...Authors: Son, J. / Jang, J. / Beyett, T.S. / Eum, Y. / Haikala, H.M. / Verano, A. / Lin, M. / Hatcher, J.M. / Kwiatkowski, N.P. / Eser, P.O. / Poitras, M.J. / Wang, S. / Xu, M. / Gokhale, P.C. / Cameron, M.D. / Eck, M.J. / Gray, N.S. / Janne, P.A.
History
DepositionAug 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Receptor tyrosine-protein kinase erbB-2
A: Receptor tyrosine-protein kinase erbB-2
C: Receptor tyrosine-protein kinase erbB-2
D: Receptor tyrosine-protein kinase erbB-2
E: Receptor tyrosine-protein kinase erbB-2
F: Receptor tyrosine-protein kinase erbB-2
G: Receptor tyrosine-protein kinase erbB-2
H: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,57716
Polymers295,0768
Non-polymers4,5018
Water00
1
B: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Receptor tyrosine-protein kinase erbB-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4472
Polymers36,8851
Non-polymers5631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.138, 154.617, 93.548
Angle α, β, γ (deg.)90.000, 102.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 713 through 740 or resid 746...
21(chain B and (resid 713 through 740 or resid 746...
31(chain C and (resid 713 through 740 or resid 746...
41(chain D and (resid 713 through 740 or resid 746...
51(chain E and (resid 713 through 740 or resid 746...
61(chain F and (resid 713 through 763 or resid 765...
71(chain G and (resid 713 through 740 or resid 746...
81(chain H and (resid 713 through 740 or resid 746...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 713 through 740 or resid 746...A713 - 740
121(chain A and (resid 713 through 740 or resid 746...A746 - 763
131(chain A and (resid 713 through 740 or resid 746...A765 - 856
141(chain A and (resid 713 through 740 or resid 746...A858 - 867
151(chain A and (resid 713 through 740 or resid 746...A975 - 991
161(chain A and (resid 713 through 740 or resid 746...A1001
211(chain B and (resid 713 through 740 or resid 746...B713 - 740
221(chain B and (resid 713 through 740 or resid 746...B746 - 763
231(chain B and (resid 713 through 740 or resid 746...B707 - 1001
241(chain B and (resid 713 through 740 or resid 746...B975 - 99
251(chain B and (resid 713 through 740 or resid 746...B975 - 991
261(chain B and (resid 713 through 740 or resid 746...B1001
311(chain C and (resid 713 through 740 or resid 746...C713 - 740
321(chain C and (resid 713 through 740 or resid 746...C746 - 763
331(chain C and (resid 713 through 740 or resid 746...C765 - 856
341(chain C and (resid 713 through 740 or resid 746...C858 - 867
351(chain C and (resid 713 through 740 or resid 746...C975 - 991
361(chain C and (resid 713 through 740 or resid 746...C1001
411(chain D and (resid 713 through 740 or resid 746...D713 - 740
421(chain D and (resid 713 through 740 or resid 746...D746 - 763
431(chain D and (resid 713 through 740 or resid 746...D765 - 856
441(chain D and (resid 713 through 740 or resid 746...D858 - 867
451(chain D and (resid 713 through 740 or resid 746...D975 - 991
461(chain D and (resid 713 through 740 or resid 746...D1001
511(chain E and (resid 713 through 740 or resid 746...E713 - 740
521(chain E and (resid 713 through 740 or resid 746...E746 - 763
531(chain E and (resid 713 through 740 or resid 746...E709 - 992
541(chain E and (resid 713 through 740 or resid 746...E858 - 867
551(chain E and (resid 713 through 740 or resid 746...E975 - 991
561(chain E and (resid 713 through 740 or resid 746...E1001
611(chain F and (resid 713 through 763 or resid 765...F713 - 763
621(chain F and (resid 713 through 763 or resid 765...F765 - 856
631(chain F and (resid 713 through 763 or resid 765...F713 - 1001
641(chain F and (resid 713 through 763 or resid 765...F885 - 973
651(chain F and (resid 713 through 763 or resid 765...F975 - 1001
711(chain G and (resid 713 through 740 or resid 746...G713 - 740
721(chain G and (resid 713 through 740 or resid 746...G746 - 763
731(chain G and (resid 713 through 740 or resid 746...G765 - 856
741(chain G and (resid 713 through 740 or resid 746...G858 - 867
751(chain G and (resid 713 through 740 or resid 746...G975 - 991
761(chain G and (resid 713 through 740 or resid 746...G1001
811(chain H and (resid 713 through 740 or resid 746...H713 - 740
821(chain H and (resid 713 through 740 or resid 746...H746 - 763
831(chain H and (resid 713 through 740 or resid 746...H765 - 856
841(chain H and (resid 713 through 740 or resid 746...H975 - 99
851(chain H and (resid 713 through 740 or resid 746...H975 - 991
861(chain H and (resid 713 through 740 or resid 746...H1001

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Components

#1: Protein
Receptor tyrosine-protein kinase erbB-2 / Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / ...Metastatic lymph node gene 19 protein / MLN 19 / Proto-oncogene Neu / Proto-oncogene c-ErbB-2 / Tyrosine kinase-type cell surface receptor HER2 / p185erbB2


Mass: 36884.512 Da / Num. of mol.: 8 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBB2, HER2, MLN19, NEU, NGL / Plasmid: pTriEX / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04626, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-VOY / (2E)-N-[3-cyano-7-ethoxy-4-({3-methyl-4-[([1,2,4]triazolo[1,5-a]pyridin-7-yl)oxy]phenyl}amino)quinolin-6-yl]-4-(dimethylamino)but-2-enamide


Mass: 562.622 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C31H30N8O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.6 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M PIPES pH 6.5, 0.3 M ammonium tartrate, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.26→91.34 Å / Num. obs: 75837 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 48.579 Å2 / Rpim(I) all: 0.226 / Rrim(I) all: 0.595 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
3.26-3.3270.91260718051.4773.9392.6
8.86-91.226.89.21372520140.0360.09599.6

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP0

3pp0


Resolution: 3.27→91.34 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2849 3908 5.15 %
Rwork0.239 71929 -
obs0.2413 75837 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.27 Å2 / Biso mean: 65.1921 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 3.27→91.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17524 0 336 0 17860
Biso mean--45.76 --
Num. residues----2190
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10107X-RAY DIFFRACTION14.928TORSIONAL
12B10107X-RAY DIFFRACTION14.928TORSIONAL
13C10107X-RAY DIFFRACTION14.928TORSIONAL
14D10107X-RAY DIFFRACTION14.928TORSIONAL
15E10107X-RAY DIFFRACTION14.928TORSIONAL
16F10107X-RAY DIFFRACTION14.928TORSIONAL
17G10107X-RAY DIFFRACTION14.928TORSIONAL
18H10107X-RAY DIFFRACTION14.928TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.27-3.310.32031410.3203246596
3.31-3.350.38831180.3503259798
3.35-3.40.38071460.345254298
3.4-3.440.37231370.3292256898
3.44-3.490.32661360.3176257299
3.49-3.540.31921310.3018256098
3.54-3.60.35511520.3032260898
3.6-3.660.30991440.3099254498
3.66-3.720.42431280.3048257498
3.72-3.790.33981470.2968255396
3.79-3.860.311370.2609254099
3.86-3.940.30871490.2636258899
3.94-4.030.32731400.25022580100
4.03-4.120.29041380.2463262299
4.12-4.220.28521420.2234257299
4.22-4.340.24861450.2118259199
4.34-4.460.2771420.214258699
4.46-4.610.24421320.1966258799
4.61-4.770.21831350.1882258298
4.77-4.960.26991400.2011252496
4.96-5.190.24181290.1982256898
5.19-5.460.26971410.2039260499
5.46-5.810.28311470.22012600100
5.81-6.250.24261480.2072257599
6.25-6.880.27291350.2086258999
6.88-7.880.23591380.2124254797
7.88-9.920.21531480.1666255899
9.93-91.340.24471420.2127253396
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4633-0.11620.76336.26262.13841.89650.0597-0.203-0.0003-0.1355-0.03210.0574-0.0815-0.1021-0.08140.3478-0.04850.0340.43640.04620.327230.8954.97241.619
21.78-0.6023-0.59475.59380.68122.98590.07130.0130.14250.2853-0.02760.0940.1758-0.0378-0.05460.2818-0.0734-0.06690.36710.07860.290765.0545.05176.392
31.3167-1.8533-0.46556.49911.42232.2814-0.13150.0566-0.0278-0.20880.08950.04660.10180.00290.01650.3757-0.1045-0.04660.38340.05420.401420.769-1.95586.023
41.0117-2.0079-0.3785.77290.83292.1620.01690.1205-0.0513-0.2726-0.03180.16150.01270.03810.03550.3051-0.0399-0.02760.35950.03350.255876.536-2.35330.099
52.5305-2.81020.29256.0818-0.61281.9987-0.02210.03590.08370.1294-0.01340.2112-0.2421-0.1080.07510.2556-0.0169-0.01580.3878-0.06260.328739.71843.75175.95
61.82030.81790.0815.4110.52641.7133-0.16410.00620.1774-0.25640.11950.7092-0.2424-0.08480.04220.46350.06340.04080.39310.06530.323265.648-33.82950.171
71.8331-1.67730.31446.1284-1.56771.4457-0.03080.0571-0.1346-0.31170.1459-0.1142-0.0172-0.054-0.15770.4356-0.07140.09280.4015-0.03630.323951.3836.61431.381
81.5134-0.62140.46994.772-2.12012.72190.0188-0.07780.20240.4382-0.2343-0.441-0.23120.22570.16410.3142-0.0607-0.05090.3285-0.02460.428686.25535.95586.485
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND ( RESID 708:996 OR RESID 1101:1101 ) )B708 - 996
2X-RAY DIFFRACTION1( CHAIN B AND ( RESID 708:996 OR RESID 1101:1101 ) )B1101
3X-RAY DIFFRACTION2( CHAIN A AND RESID 706:992 )A706 - 992
4X-RAY DIFFRACTION3( CHAIN C AND RESID 710:992 )C710 - 992
5X-RAY DIFFRACTION4( CHAIN D AND RESID 710:992 )D710 - 992
6X-RAY DIFFRACTION5( CHAIN E AND RESID 709:992 )E709 - 992
7X-RAY DIFFRACTION6( CHAIN F AND ( RESID 713:991 OR RESID 1101:1101 ) )F713 - 991
8X-RAY DIFFRACTION6( CHAIN F AND ( RESID 713:991 OR RESID 1101:1101 ) )F1101
9X-RAY DIFFRACTION7( CHAIN G AND RESID 706:992 )G706 - 992
10X-RAY DIFFRACTION8( CHAIN H AND RESID 707:992 )H707 - 992

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Yorodumi

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  • 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

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