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- PDB-4dz6: Transition state mimic of nucleoside-diphosphate kinase from borr... -

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Basic information

Entry
Database: PDB / ID: 4dz6
TitleTransition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp
ComponentsNucleoside diphosphate kinaseNucleoside-diphosphate kinase
KeywordsTRANSFERASE / SSGCID / NIAID / NUCLEOSIDE DIPHOSPHATE KINASE / KINASE / VANADATE / TRANSITION STATE MIMIC / TRANSITION STATE ANALOG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / oxido(dioxo)vanadium / VANADATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Structure and analysis of nucleoside diphosphate kinase from Borrelia burgdorferi prepared in a transition-state complex with ADP and vanadate moieties.
Authors: Dumais, M. / Davies, D.R. / Lin, T. / Staker, B.L. / Myler, P.J. / Van Voorhis, W.C.
History
DepositionFeb 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,21117
Polymers130,1646
Non-polymers2,04711
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23080 Å2
ΔGint-100 kcal/mol
Surface area35680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.650, 81.000, 181.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 21693.934 Da / Num. of mol.: 6 / Fragment: NUCLEOSIDE-DIPHOSPHATE KINASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: ndk, BB_0463 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O51419, nucleoside-diphosphate kinase

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Non-polymers , 5 types, 339 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: VO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsFOR CHAINS B, E AND F THE LIGANDS TENTATIVELY IDENTIFIED AS VO4 COULD NOT BE MODELED AS ADP OR ANY ...FOR CHAINS B, E AND F THE LIGANDS TENTATIVELY IDENTIFIED AS VO4 COULD NOT BE MODELED AS ADP OR ANY OTHER COMPONENT OF THE CRYSTALLIZATION DROP

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: EBS INTERNAL TRACKING NUMBER ACTIVATED SODIUM ORTHOVANADATE, 2 MM ADP, BOBUA.00664.A.A1_ PS00257 AT 17 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 / Wavelength: 0.97856 Å
DetectorType: MARCCD 300 / Detector: CCD / Date: Feb 9, 2012
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.978561
ReflectionResolution: 2.2→99.47 Å / Num. obs: 87269 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.87 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.32
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.6 / % possible all: 99.47

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4DI6
Resolution: 2.2→99.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 10.775 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3003 5.1 %RANDOM
Rwork0.183 ---
obs0.185 59351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.587 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---1.51 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→99.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8065 0 116 328 8509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198394
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.96911366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80851012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3823.466378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.017151459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.851553
X-RAY DIFFRACTIONr_chiral_restr0.0980.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216256
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 197 -
Rwork0.234 3868 -
obs--99.73 %
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)
12.591-0.5373-0.85080.5724-0.05670.4371-0.0019-0.0847-0.14820.0343-0.00290.0755-0.01090.00230.00480.0606-0.02010.02010.04480.01060.03419.256724.566122.8614
21.64440.3155-0.51620.5991-0.36481.33170.0175-0.1475-0.001-0.0474-0.05150.11130.1040.0130.03390.037-0.00620.02350.0168-0.0130.064515.290721.922519.227
31.50230.252-2.18661.2159-1.1613.7625-0.1877-0.2206-0.0615-0.06670.0174-0.0640.40050.28120.17040.2229-0.00450.06140.05070.02470.079212.629310.952235.2347
41.11820.0271-0.60040.48880.2041.7054-0.074-0.1231-0.13890.08650.04070.04870.0580.2080.03330.05740.00090.03730.0340.0080.037621.708324.727430.9548
51.1374-0.0734-1.18220.5605-0.49292.2729-0.0232-0.0507-0.17390.00920.00520.09350.2393-0.01220.01790.1311-0.03730.00140.01510.00670.104716.707216.047525.4715
66.96710.19672.57181.19950.25431.4630.01070.1431-0.0635-0.1819-0.01940.00670.04140.1640.00870.04940.01020.02280.0761-0.01960.037231.664325.73747.8783
72.7120.1222-0.75570.15490.33551.1897-0.02150.08660.0403-0.0141-0.03360.0467-0.0426-0.06840.05510.0569-0.0070.0150.0454-0.01740.06719.831935.517513.5108
80.83250.0617-0.27071.71630.00760.08850.0633-0.0822-0.0408-0.14-0.07720.0112-0.0230.02470.01390.0448-0.0149-0.0290.0572-0.01910.05697.498825.7451.591
98.8769-2.84665.16020.9408-1.64474.1939-0.08570.39230.1535-0.0257-0.065-0.0127-0.05810.32480.15070.1481-0.0948-0.08240.13020.03860.11368.39833.2094-7.7981
100.5907-0.753-0.99421.25631.15422.0668-0.04510.1469-0.09170.0877-0.08640.2164-0.0278-0.18750.13150.0374-0.0189-0.00290.1112-0.00940.09174.681436.595712.29
111.08340.7859-0.49451.32670.49523.2162-0.05980.18010.1841-0.04770.02640.1256-0.0664-0.06780.03340.0452-0.0034-0.00640.05630.04290.043117.244743.74050.4832
120.6608-0.17260.01980.58830.68132.83820.01680.0218-0.06830.0103-0.03730.22370.0431-0.30910.02050.0134-0.02340.01740.0713-0.00830.13590.692131.89715.0284
131.1358-0.00850.23911.53521.21681.57770.0299-0.01450.1159-0.00350.02-0.10410.00640.1396-0.04990.0394-0.03190.02780.0577-0.01250.076639.546842.972819.7214
141.27290.20581.08493.36210.11120.94230.12760.2129-0.1527-0.30490.0155-0.37750.07930.2296-0.14310.0938-0.06430.05950.1919-0.05540.232251.932740.047110.8404
1510.6425-5.62336.39269.8926-2.70593.9051-0.2486-0.06790.28820.96040.1544-1.0568-0.0708-0.03330.09410.2039-0.002-0.06180.1724-0.04460.180656.905125.313317.7845
160.7474-0.0368-0.29861.86420.26940.17270.0526-0.16050.04050.04940.028-0.306-0.01910.1193-0.08060.012-0.02310.01940.1812-0.06880.147146.977138.808418.2063
170.6643-0.0592-0.31561.2106-0.05190.61970.0085-0.08150.06360.11650.0364-0.21610.05890.1935-0.04480.03460.0039-0.00690.1068-0.04030.098144.784834.632119.3454
181.7189-0.2371-0.94162.5492-2.44663.16990.1751-0.30360.24750.2787-0.1003-0.1362-0.43210.3541-0.07480.1421-0.13570.02440.1782-0.12580.242140.316557.557432.0468
191.3620.82990.12060.7552-0.2860.75870.1333-0.09570.11310.2047-0.02670.0634-0.2316-0.0542-0.10650.1286-0.00730.08380.0196-0.02680.120312.605655.698831.2208
201.4916-0.28610.24110.15660.09590.65480.0322-0.16550.20150.00090.0679-0.1093-0.1595-0.1363-0.10.19270.03120.09650.0978-0.0550.13585.242459.089837.5351
2123.381-2.61011.185911.2368-8.04165.9027-0.04350.78130.0999-0.08850.0530.086-0.1688-0.1452-0.00950.47540.0799-0.03810.2891-0.11120.0693-9.788661.741428.3393
221.78950.0636-0.35780.06960.19050.72880.0637-0.10220.2143-0.0239-0.04750.0227-0.1711-0.1317-0.01620.16880.03360.07320.0617-0.0560.13666.219358.229931.9851
231.23160.33180.18431.18250.86871.06110.08690.0320.1693-0.0509-0.08610.2075-0.1603-0.1285-0.00070.10550.02410.07290.02940.00030.12513.218655.444927.9158
242.3361-0.8201-2.73410.47210.33475.36620.0892-0.05690.21410.0804-0.0129-0.1282-0.40320.2091-0.07630.2209-0.08750.06830.0543-0.07480.197227.376765.766631.5955
250.34480.10150.34850.6761-0.22810.5603-0.04220.05080.0723-0.02320.0004-0.0619-0.07730.06710.04180.0778-0.04480.06640.0510.00150.156331.813154.072711.004
260.2999-0.12180.13161.58290.09090.09750.00190.1440.11710.02070.0149-0.2386-0.05440.0891-0.01680.1522-0.05710.08720.09850.0250.181538.066359.30927.7489
275.0484-3.45212.99017.9168-3.11715.2055-0.02170.28210.27420.35370.16120.2986-0.29190.089-0.13950.1616-0.04680.12670.10550.07760.311833.013973.56888.2538
282.46490.97070.50161.480.78720.72650.01240.12530.284-0.2909-0.0175-0.0782-0.33710.03610.00520.2006-0.02720.04520.05050.02820.144530.892154.40385.9623
291.3032-0.6397-0.65091.81960.60151.97980.05350.020.2545-0.07350-0.0228-0.32670.0055-0.05350.1488-0.03920.05570.02360.00450.160327.96863.306311.2206
304.50211.04631.7651.88170.89480.8442-0.02660.31650.0573-0.24120.0798-0.1423-0.09740.1343-0.05320.0762-0.02040.0740.0983-0.01090.080433.372340.23080.0729
311.68911.2021-0.86433.5359-1.1240.54820.0076-0.2180.020.3511-0.0108-0.064-0.09630.09140.00320.1351-0.02640.01490.0858-0.04420.031823.481746.914741.1785
320.8520.2957-0.22020.7797-0.12450.175-0.008-0.26420.05870.35290.0256-0.0184-0.05380.1533-0.01760.2448-0.00310.02170.2136-0.06560.043223.537650.766448.5842
3324.2518-6.48384.46321.7431-1.19460.8234-0.3038-1.1596-2.2010.19940.51870.5216-0.1058-0.1892-0.21490.80430.1501-0.3530.5856-0.07260.701740.544748.845956.9861
341.96840.02180.23021.37580.25750.1076-0.105-0.25640.05060.36260.12860.00090.00380.0715-0.02360.2589-0.0592-0.00480.2238-0.07420.047726.485247.273946.7506
351.1242-0.516-0.18770.5552-0.61451.95490.0446-0.22090.15230.1190.0177-0.1079-0.10060.2236-0.06230.1954-0.0722-0.05360.1236-0.07220.109734.838345.469143.259
361.70030.26030.4062.5981.54211.5695-0.0609-0.26090.0980.3349-0.05310.3055-0.0188-0.19210.1140.16450.01260.0850.1073-0.01290.061710.383241.76445.593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 29
2X-RAY DIFFRACTION2A30 - 47
3X-RAY DIFFRACTION3A48 - 75
4X-RAY DIFFRACTION4A76 - 122
5X-RAY DIFFRACTION5A123 - 157
6X-RAY DIFFRACTION6A158 - 169
7X-RAY DIFFRACTION7B2 - 35
8X-RAY DIFFRACTION8B36 - 55
9X-RAY DIFFRACTION9B56 - 77
10X-RAY DIFFRACTION10B78 - 95
11X-RAY DIFFRACTION11B96 - 131
12X-RAY DIFFRACTION12B132 - 169
13X-RAY DIFFRACTION13C5 - 35
14X-RAY DIFFRACTION14C36 - 55
15X-RAY DIFFRACTION15C56 - 66
16X-RAY DIFFRACTION16C67 - 95
17X-RAY DIFFRACTION17C96 - 157
18X-RAY DIFFRACTION18C158 - 169
19X-RAY DIFFRACTION19D2 - 30
20X-RAY DIFFRACTION20D31 - 56
21X-RAY DIFFRACTION21D57 - 66
22X-RAY DIFFRACTION22D67 - 96
23X-RAY DIFFRACTION23D97 - 154
24X-RAY DIFFRACTION24D155 - 169
25X-RAY DIFFRACTION25E3 - 29
26X-RAY DIFFRACTION26E30 - 55
27X-RAY DIFFRACTION27E56 - 75
28X-RAY DIFFRACTION28E76 - 96
29X-RAY DIFFRACTION29E97 - 152
30X-RAY DIFFRACTION30E153 - 169
31X-RAY DIFFRACTION31F3 - 28
32X-RAY DIFFRACTION32F29 - 56
33X-RAY DIFFRACTION33F57 - 66
34X-RAY DIFFRACTION34F67 - 96
35X-RAY DIFFRACTION35F97 - 146
36X-RAY DIFFRACTION36F147 - 169

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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

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