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- PDB-5hzn: Structure of NVP-AEW541 in complex with IGF-1R kinase -

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Basic information

Entry
Database: PDB / ID: 5hzn
TitleStructure of NVP-AEW541 in complex with IGF-1R kinase
ComponentsInsulin-like growth factor 1 receptor
KeywordsTRANSFERASE / Inhibitor / Kinase
Function / homology
Function and homology information


cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / protein transporter activity / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / protein transporter activity / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / insulin binding / response to L-glutamate / negative regulation of MAPK cascade / establishment of cell polarity / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of osteoblast proliferation / positive regulation of cytokinesis / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / estrous cycle / G-protein alpha-subunit binding / response to vitamin E / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to dexamethasone stimulus / cerebellum development / axonogenesis / insulin-like growth factor receptor signaling pathway / caveola / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / response to nicotine / receptor protein-tyrosine kinase / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / response to ethanol / positive regulation of MAPK cascade / protein autophosphorylation / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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 ...Tyrosine-protein kinase, insulin-like receptor / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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 / : / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / 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-66A / Insulin-like growth factor 1 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsCowan-Jacob, S.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors.
Authors: Stauffer, F. / Cowan-Jacob, S.W. / Scheufler, C. / Furet, P.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Refinement description
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-like growth factor 1 receptor
B: Insulin-like growth factor 1 receptor
C: Insulin-like growth factor 1 receptor
D: Insulin-like growth factor 1 receptor
E: Insulin-like growth factor 1 receptor
F: Insulin-like growth factor 1 receptor
G: Insulin-like growth factor 1 receptor
H: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,32528
Polymers276,8628
Non-polymers5,46320
Water9,926551
1
A: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3394
Polymers34,6081
Non-polymers7313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2433
Polymers34,6081
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3394
Polymers34,6081
Non-polymers7313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2433
Polymers34,6081
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3394
Polymers34,6081
Non-polymers7313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2433
Polymers34,6081
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3394
Polymers34,6081
Non-polymers7313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Insulin-like growth factor 1 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2433
Polymers34,6081
Non-polymers6352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.435, 190.045, 155.488
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H
15A
25B
35C
45D
16E
26F
36G
46H
17A
27B
37C
47D
18E
28F
38G
48H
19A
29B
39C
49D
110E
210F
310G
410H
111A
211B
311C
411D
112E
212F
312G
412H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALACYSCYS1AA980 - 10561 - 77
211ALAALACYSCYS1EE980 - 10561 - 77
121ARGARGGLYGLY1AA1131 - 1149152 - 170
221ARGARGGLYGLY1EE1131 - 1149152 - 170
131PHEPHELYSLYS1AA1151 - 1283172 - 304
231PHEPHELYSLYS1EE1151 - 1283172 - 304
141HISHISVALVAL1AA1058 - 112979 - 150
241HISHISVALVAL1EE1058 - 112979 - 150
112ALAALACYSCYS1BB980 - 10561 - 77
212ALAALACYSCYS1FF980 - 10561 - 77
122ARGARGGLYGLY1BB1131 - 1149152 - 170
222ARGARGGLYGLY1FF1131 - 1149152 - 170
132PHEPHELYSLYS1BB1151 - 1283172 - 304
232PHEPHELYSLYS1FF1151 - 1283172 - 304
142HISHISVALVAL1BB1058 - 112979 - 150
242HISHISVALVAL1FF1058 - 112979 - 150
113ALAALALYSLYS1CC980 - 12831 - 304
213ALAALALYSLYS1GG980 - 12831 - 304
114ALAALACYSCYS1DD980 - 10561 - 77
214ALAALACYSCYS1HH980 - 10561 - 77
124HISHISGLYGLY1DD1058 - 114979 - 170
224HISHISGLYGLY1HH1058 - 114979 - 170
134PHEPHEASNASN1DD1151 - 1282172 - 303
234PHEPHEASNASN1HH1151 - 1282172 - 303
115ASPASPGLYGLY4AA982 - 10033 - 24
215ASPASPGLYGLY4BB982 - 10033 - 24
315ASPASPGLYGLY4CC982 - 10033 - 24
415ASPASPGLYGLY4DD982 - 10033 - 24
125GLYGLYVALVAL4AA1005 - 103226 - 53
225GLYGLYVALVAL4BB1005 - 103226 - 53
325GLYGLYVALVAL4CC1005 - 103226 - 53
425GLYGLYVALVAL4DD1005 - 103226 - 53
116ASPASPGLYGLY4EE982 - 10033 - 24
216ASPASPGLYGLY4FF982 - 10033 - 24
316ASPASPGLYGLY4GG982 - 10033 - 24
416ASPASPGLYGLY4HH982 - 10033 - 24
126GLYGLYVALVAL4EE1005 - 103226 - 53
226GLYGLYVALVAL4FF1005 - 103226 - 53
326GLYGLYVALVAL4GG1005 - 103226 - 53
426GLYGLYVALVAL4HH1005 - 103226 - 53
117ILEILEARGARG4AA1042 - 109263 - 113
217ILEILEARGARG4BB1042 - 109263 - 113
317ILEILEARGARG4CC1042 - 109263 - 113
417ILEILEARGARG4DD1042 - 109263 - 113
118ILEILEARGARG4EE1042 - 109263 - 113
218ILEILEARGARG4FF1042 - 109263 - 113
318ILEILEARGARG4GG1042 - 109263 - 113
418ILEILEARGARG4HH1042 - 109263 - 113
119ALAALALEULEU4AA1102 - 1170123 - 191
219ALAALALEULEU4BB1102 - 1170123 - 191
319ALAALALEULEU4CC1102 - 1170123 - 191
419ALAALALEULEU4DD1102 - 1170123 - 191
1110ALAALALEULEU4EE1102 - 1170123 - 191
2110ALAALALEULEU4FF1102 - 1170123 - 191
3110ALAALALEULEU4GG1102 - 1170123 - 191
4110ALAALALEULEU4HH1102 - 1170123 - 191
1111LEULEUSERSER4AA1171 - 1279192 - 300
2111LEULEUSERSER4BB1171 - 1279192 - 300
3111LEULEUSERSER4CC1171 - 1279192 - 300
4111LEULEUSERSER4DD1171 - 1279192 - 300
1112LEULEUSERSER4EE1171 - 1279192 - 300
2112LEULEUSERSER4FF1171 - 1279192 - 300
3112LEULEUSERSER4GG1171 - 1279192 - 300
4112LEULEUSERSER4HH1171 - 1279192 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

#1: Protein
Insulin-like growth factor 1 receptor / Insulin-like growth factor I receptor / IGF-I receptor


Mass: 34607.758 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Production host: unidentified baculovirus
References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-66A / 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 439.552 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H29N5O
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97779 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 147785 / % possible obs: 90.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/av σ(I): 16.638 / Net I/σ(I): 9.8
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.280.413178.5
2.28-2.370.304178.6
2.37-2.480.238181
2.48-2.610.19186.9
2.61-2.770.147191.8
2.77-2.990.118195.9
2.99-3.290.097198.3
3.29-3.760.079199.2
3.76-4.740.064199.4
4.74-400.054199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.491 / Cor.coef. Fo:Fc: 0.36
Highest resolutionLowest resolution
Rotation4 Å38.87 Å
Translation4 Å38.87 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.1.9999refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.71 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2567 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 7403 5 %RANDOM
Rwork0.194 ---
obs0.1952 140330 90.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 91.49 Å2 / Biso mean: 45.611 Å2 / Biso min: 17.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20.05 Å2
2--2.95 Å20 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18975 0 380 551 19906
Biso mean--50.34 42.78 -
Num. residues----2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02219811
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.97626749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14852361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3223.947912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.003153476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.62115144
X-RAY DIFFRACTIONr_chiral_restr0.0830.22827
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214988
X-RAY DIFFRACTIONr_nbd_refined0.20.29022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2971
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.226
X-RAY DIFFRACTIONr_mcbond_it1.072212277
X-RAY DIFFRACTIONr_mcangle_it1.712319094
X-RAY DIFFRACTIONr_scbond_it2.22748824
X-RAY DIFFRACTIONr_scangle_it3.44567623
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2331TIGHT POSITIONAL0.050.05
1A2331TIGHT THERMAL0.170.5
2B2331TIGHT POSITIONAL0.060.05
2B2331TIGHT THERMAL0.250.5
3C2359TIGHT POSITIONAL0.060.05
3C2359TIGHT THERMAL0.210.5
4D2396TIGHT POSITIONAL0.080.05
4D2396TIGHT THERMAL0.180.5
5A390MEDIUM POSITIONAL0.420.5
5B390MEDIUM POSITIONAL0.450.5
5C390MEDIUM POSITIONAL0.390.5
5D390MEDIUM POSITIONAL0.580.5
5A390MEDIUM THERMAL2.122
5B390MEDIUM THERMAL1.462
5C390MEDIUM THERMAL1.82
5D390MEDIUM THERMAL1.582
6E390MEDIUM POSITIONAL0.420.5
6F390MEDIUM POSITIONAL0.450.5
6G390MEDIUM POSITIONAL0.390.5
6H390MEDIUM POSITIONAL0.580.5
6E390MEDIUM THERMAL2.192
6F390MEDIUM THERMAL1.522
6G390MEDIUM THERMAL1.692
6H390MEDIUM THERMAL1.542
7A408MEDIUM POSITIONAL0.310.5
7B408MEDIUM POSITIONAL0.340.5
7C408MEDIUM POSITIONAL0.310.5
7D408MEDIUM POSITIONAL0.380.5
7A408MEDIUM THERMAL1.72
7B408MEDIUM THERMAL1.592
7C408MEDIUM THERMAL1.52
7D408MEDIUM THERMAL1.712
8E408MEDIUM POSITIONAL0.30.5
8F408MEDIUM POSITIONAL0.350.5
8G408MEDIUM POSITIONAL0.30.5
8H408MEDIUM POSITIONAL0.370.5
8E408MEDIUM THERMAL1.642
8F408MEDIUM THERMAL1.632
8G408MEDIUM THERMAL1.312
8H408MEDIUM THERMAL1.622
9A530MEDIUM POSITIONAL0.320.5
9B530MEDIUM POSITIONAL0.250.5
9C530MEDIUM POSITIONAL0.370.5
9D530MEDIUM POSITIONAL0.310.5
9A530MEDIUM THERMAL1.62
9B530MEDIUM THERMAL1.62
9C530MEDIUM THERMAL1.42
9D530MEDIUM THERMAL1.852
10E530MEDIUM POSITIONAL0.310.5
10F530MEDIUM POSITIONAL0.240.5
10G530MEDIUM POSITIONAL0.390.5
10H530MEDIUM POSITIONAL0.30.5
10E530MEDIUM THERMAL1.652
10F530MEDIUM THERMAL1.542
10G530MEDIUM THERMAL1.432
10H530MEDIUM THERMAL1.742
11A898MEDIUM POSITIONAL0.260.5
11B898MEDIUM POSITIONAL0.290.5
11C898MEDIUM POSITIONAL0.260.5
11D898MEDIUM POSITIONAL0.280.5
11A898MEDIUM THERMAL1.712
11B898MEDIUM THERMAL1.532
11C898MEDIUM THERMAL1.492
11D898MEDIUM THERMAL1.32
12E898MEDIUM POSITIONAL0.260.5
12F898MEDIUM POSITIONAL0.290.5
12G898MEDIUM POSITIONAL0.260.5
12H898MEDIUM POSITIONAL0.290.5
12E898MEDIUM THERMAL1.72
12F898MEDIUM THERMAL1.452
12G898MEDIUM THERMAL1.412
12H898MEDIUM THERMAL1.282
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.271 428
Rwork0.237 8563
all-8991

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