[English] 日本語
Yorodumi
- PDB-7vdp: The structure of cyclin-dependent kinase 5 (CDK5) in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vdp
TitleThe structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1
Components
  • Cyclin-dependent kinase 5 activator 1, p25
  • Cyclin-dependent-like kinase 5
KeywordsTRANSFERASE / CDK5 / p25
Function / homology
Function and homology information


superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 ...superior olivary nucleus maturation / protein kinase 5 complex / acetylcholine receptor activator activity / G1 to G0 transition involved in cell differentiation / ErbB-2 class receptor binding / negative regulation of synaptic plasticity / contractile muscle fiber / positive regulation of calcium ion-dependent exocytosis / neuron cell-cell adhesion / Activated NTRK2 signals through CDK5 / layer formation in cerebral cortex / negative regulation of axon extension / protein localization to synapse / receptor catabolic process / regulation of synaptic vesicle cycle / corpus callosum development / cerebellar cortex formation / regulation of dendritic spine morphogenesis / CRMPs in Sema3A signaling / NGF-stimulated transcription / synaptic transmission, dopaminergic / ErbB-3 class receptor binding / negative regulation of protein export from nucleus / axon extension / cyclin-dependent protein serine/threonine kinase activator activity / axonal fasciculation / motor neuron axon guidance / calcium ion import / regulation of synaptic vesicle recycling / embryo development ending in birth or egg hatching / dendrite morphogenesis / regulation of neuron differentiation / receptor clustering / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / synaptic vesicle transport / regulation of cyclin-dependent protein serine/threonine kinase activity / tau-protein kinase activity / protein kinase activator activity / beta-tubulin binding / central nervous system neuron development / oligodendrocyte differentiation / synaptic vesicle exocytosis / behavioral response to cocaine / negative regulation of cell cycle / synaptic vesicle endocytosis / DARPP-32 events / positive regulation of protein targeting to membrane / ephrin receptor signaling pathway / alpha-tubulin binding / regulation of protein localization to plasma membrane / regulation of macroautophagy / cyclin-dependent protein serine/threonine kinase activity / Schwann cell development / phosphorylation / cyclin-dependent protein kinase holoenzyme complex / skeletal muscle tissue development / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / negative regulation of protein ubiquitination / positive regulation of microtubule polymerization / synapse assembly / sensory perception of pain / NPAS4 regulates expression of target genes / ephrin receptor binding / regulation of cell migration / ionotropic glutamate receptor signaling pathway / cell-matrix adhesion / axonogenesis / protein serine/threonine kinase activator activity / cerebellum development / excitatory postsynaptic potential / filopodium / axon guidance / synaptic transmission, glutamatergic / hippocampus development / negative regulation of proteolysis / regulation of actin cytoskeleton organization / peptidyl-threonine phosphorylation / intracellular protein transport / neuron migration / brain development / Hsp90 protein binding / neuromuscular junction / visual learning / tau protein binding / regulation of synaptic plasticity / neuron differentiation / G protein-coupled acetylcholine receptor signaling pathway / microtubule cytoskeleton organization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / neuron projection development / actin filament binding / rhythmic process / p53 binding / cell junction / lamellipodium / kinase activity / presynapse / Factors involved in megakaryocyte development and platelet production
Similarity search - Function
Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / : / 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. ...Cyclin-dependent kinase 5 activator / Cyclin-dependent kinase 5 activator protein / Cyclin-like superfamily / : / 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
Similarity search - Domain/homology
Chem-65L / DI(HYDROXYETHYL)ETHER / Cyclin-dependent kinase 5 / Cyclin-dependent kinase 5 activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMalojcic, G. / Clugston, S.L. / Daniels, M. / Harmange, J.C. / Ledeborer, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Discovery and Optimization of Highly Selective Inhibitors of CDK5.
Authors: Daniels, M.H. / Malojcic, G. / Clugston, S.L. / Williams, B. / Coeffet-Le Gal, M. / Pan-Zhou, X.R. / Venkatachalan, S. / Harmange, J.C. / Ledeboer, M.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Cyclin-dependent-like kinase 5
B: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,31926
Polymers113,2764
Non-polymers2,04222
Water6,702372
1
A: Cyclin-dependent-like kinase 5
C: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,24623
Polymers56,6382
Non-polymers1,60821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-60 kcal/mol
Surface area19390 Å2
MethodPISA
2
B: Cyclin-dependent-like kinase 5
D: Cyclin-dependent kinase 5 activator 1, p25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0733
Polymers56,6382
Non-polymers4341
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-19 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.370, 118.370, 155.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSASPASPAA3 - 2883 - 288
21LYSLYSASPASPBB3 - 2883 - 288
12SERSERSERSERCC147 - 29349 - 195
22SERSERSERSERDD147 - 29349 - 195

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Cyclin-dependent-like kinase 5 / Cell division protein kinase 5


Mass: 33306.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5, CDKN5 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q00535, non-specific serine/threonine protein kinase
#2: Protein Cyclin-dependent kinase 5 activator 1, p25


Mass: 23331.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK5R1, CDK5R, NCK5A / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15078

-
Non-polymers , 6 types, 394 molecules

#3: Chemical ChemComp-65L / [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol


Mass: 434.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23FN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07809 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07809 Å / Relative weight: 1
ReflectionResolution: 2.09→51.79 Å / Num. obs: 74979 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.018 / Rrim(I) all: 0.081 / Net I/σ(I): 24.9 / Num. measured all: 1501558
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.09-2.1418.41.42310144855250.7820.3391.4642.4100
9.35-51.79180.0281701794710.0060.02875.899.4

-
Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o0g

3o0g


Resolution: 2.09→51.79 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.865 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 3645 4.9 %RANDOM
Rwork0.2009 ---
obs0.2022 71280 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 188.45 Å2 / Biso mean: 63.908 Å2 / Biso min: 27.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å2-0 Å2
2---0.17 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 2.09→51.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6820 0 131 372 7323
Biso mean--61.62 54.52 -
Num. residues----845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137095
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176824
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.6579580
X-RAY DIFFRACTIONr_angle_other_deg1.2091.5915734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16622.055365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.609151241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561546
X-RAY DIFFRACTIONr_chiral_restr0.0660.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027807
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021619
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85960.11
12B85960.11
21C36440.17
22D36440.17
LS refinement shellResolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 260 -
Rwork0.256 5252 -
all-5512 -
obs--99.87 %
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)
18.84571.5974.11958.15452.183811.95690.1499-0.1396-0.43590.2947-0.1133-0.35580.58690.3411-0.03650.31110.04240.0310.1822-0.02360.312453.0003-47.046449.2382
23.19310.9219-0.29592.69970.41171.7711-0.0647-0.0628-0.3140.08680.0644-0.17220.23120.02490.00030.1027-0.013-0.03530.0849-0.00680.057447.4152-32.684854.072
32.309-0.02521.08631.89190.71474.574-0.0934-0.11350.09680.11260.0772-0.0012-0.165-0.08350.01620.12190.0077-0.05330.0236-0.03210.092452.8944-13.344965.7218
47.32365.27171.26577.1313-3.05274.9310.934-1.43630.22440.7649-0.39070.58040.0919-1.0587-0.54330.92770.44690.21521.45820.17851.039857.9523-44.11777.7914
56.65723.8920.02384.9812.18652.8423-0.4116-1.0873-0.85970.40290.01120.33690.4933-0.26910.40040.71080.27810.22170.91840.44960.704766.6368-52.734470.5765
64.8212-2.3003-0.78953.60580.87423.0136-0.4282-0.6686-0.20690.46250.4210.08520.31230.21660.00720.16730.1143-0.00980.3455-0.02610.160976.3641-40.069160.2775
72.007-3.5096-1.09148.3721-0.99995.01220.28320.11630.5483-0.4909-0.1689-0.9301-0.42090.298-0.11430.33830.0214-0.00830.52420.0580.367986.9281-40.401440.1393
83.29940.40010.10617.41944.00494.6085-0.1024-0.41370.87120.07390.3462-0.5637-0.4530.7022-0.24380.18490.0747-0.060.5221-0.21590.48989.2194-32.565358.9483
95.14873.28644.15318.63283.575.97290.0439-0.33790.52520.2973-0.13840.6169-0.4817-0.43860.09450.1617-0.02220.09210.3034-0.00530.136815.8839-38.134773.2412
102.1061-1.57050.77031.2047-0.77268.54590.099-0.2986-0.2111-0.0040.24380.20980.2502-0.3163-0.34280.1955-0.07840.05120.2580.06850.142712.0507-52.824369.5277
118.35551.81051.72592.48050.55770.4268-0.1564-0.299-0.04150.09990.0973-0.0273-0.0832-0.02950.05910.2906-0.0496-0.00710.27030.02980.122126.79-43.534179.7139
126.8049-3.46092.78845.5105-1.91142.64850.0007-0.15310.13210.21080.0365-0.2519-0.09960.1207-0.03720.2709-0.0681-0.0030.3012-0.00660.184735.7255-37.11478.4856
132.67392.39470.04213.3012-0.4251.19220.1-0.06130.00410.0455-0.04090.045-0.0982-0.055-0.05910.082-0.05480.00290.16160.00930.003724.7024-42.234666.9253
143.6862.39730.23838.1223-0.96473.5884-0.28760.1513-0.0715-0.38590.2501-0.6673-0.44190.47140.03760.2151-0.083-0.00980.42560.00940.225340.1054-39.037371.7298
152.44042.1932-0.35814.2972-1.22664.5536-0.1138-0.0916-0.4194-0.37720.0702-0.29010.63710.0820.04370.1125-0.04010.0180.1920.00880.088931.3891-44.187762.3615
167.32482.8602-3.69036.2691-3.53017.69630.12350.14410.6890.30770.1480.8269-0.3363-0.3732-0.27150.18050.07120.04630.212-0.01450.289417.5161-28.20865.9425
172.9615-0.02282.05390.0122-0.01541.49210.22280.4687-0.14940.06040.0577-0.07470.17650.0876-0.28051.25810.07810.12451.23540.12621.323674.1048-84.918161.538
185.9553-3.42963.43042.2613-1.8797.2326-0.1951-0.2802-1.2889-0.25130.55510.79141.3872-0.8442-0.361.4164-0.37950.07710.9482-0.12721.539268.7993-71.40750.9516
191.78471.56910.99561.9658-0.24342.85210.2596-0.0741-0.07880.04260.0224-0.02670.14150.0172-0.2820.76610.07860.10720.67340.08820.902378.0607-71.379265.397
201.8374-0.2708-0.93310.07190.13390.50170.34470.33570.6911-0.1924-0.05960.0254-0.0735-0.2851-0.28511.20180.09080.12170.96770.15921.39666.4954-73.799965.1445
215.04024.46232.7484.25652.17631.8562-0.234-0.6129-1.4544-0.55420.133-1.6105-0.0781-0.7250.1011.19290.09060.58151.1543-0.05682.456962.6957-65.357461.3121
221.40830.9717-1.68067.7050.62372.6033-0.19590.146-0.47830.54930.0654-1.10280.6746-0.09090.13050.92390.3439-0.03080.89640.34731.3180.771-68.100669.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 157
3X-RAY DIFFRACTION3A158 - 291
4X-RAY DIFFRACTION4B3 - 31
5X-RAY DIFFRACTION5B32 - 74
6X-RAY DIFFRACTION6B75 - 219
7X-RAY DIFFRACTION7B220 - 247
8X-RAY DIFFRACTION8B248 - 288
9X-RAY DIFFRACTION9C146 - 162
10X-RAY DIFFRACTION10C163 - 170
11X-RAY DIFFRACTION11C171 - 187
12X-RAY DIFFRACTION12C188 - 197
13X-RAY DIFFRACTION13C198 - 237
14X-RAY DIFFRACTION14C238 - 245
15X-RAY DIFFRACTION15C246 - 277
16X-RAY DIFFRACTION16C278 - 293
17X-RAY DIFFRACTION17D147 - 173
18X-RAY DIFFRACTION18D174 - 197
19X-RAY DIFFRACTION19D198 - 211
20X-RAY DIFFRACTION20D212 - 234
21X-RAY DIFFRACTION21D235 - 259
22X-RAY DIFFRACTION22D260 - 293

+
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