[English] 日本語
Yorodumi
- PDB-5ijs: Crystal structure of autotaxin with orthovanadate bound as a trig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ijs
TitleCrystal structure of autotaxin with orthovanadate bound as a trigonal bipyramidal intermediate analog
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2
KeywordsHYDROLASE / LYSOPHOSPHATIDYLCHOLINE / SOMATOMEDIN / INFLAMMATION / METASTASIS / NEUROPATHIC PAIN / VASCULAR DEVELOPMENT / NEURAL DEVELOPMENT
Function / homology
Function and homology information


response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phosphatidylcholine catabolic process / phospholipid catabolic process / D-type glycerophospholipase activity / positive regulation of lamellipodium morphogenesis / negative regulation of cell-matrix adhesion / phosphodiesterase I activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phosphatidylcholine catabolic process / phospholipid catabolic process / D-type glycerophospholipase activity / positive regulation of lamellipodium morphogenesis / negative regulation of cell-matrix adhesion / phosphodiesterase I activity / phosphatidylcholine lysophospholipase A1 activity / scavenger receptor activity / positive regulation of oligodendrocyte differentiation / cellular response to cadmium ion / polysaccharide binding / alkylglycerophosphoethanolamine phosphodiesterase activity / phospholipid metabolic process / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / positive regulation of substrate adhesion-dependent cell spreading / estrous cycle / regulation of cell migration / cellular response to estradiol stimulus / cell chemotaxis / nucleic acid binding / immune response / positive regulation of cell population proliferation / calcium ion binding / : / zinc ion binding / membrane
Similarity search - Function
Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Factor Xa Inhibitor / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily ...Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Factor Xa Inhibitor / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7alpha-hydroxycholesterol / IODIDE ION / VANADATE ION / Autotaxin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsHausmann, J. / Joosten, R.P. / Perrakis, A.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
KWF Netherlands
NWO Netherlands
NWO723.013.003 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural snapshots of the catalytic cycle of the phosphodiesterase Autotaxin.
Authors: Hausmann, J. / Keune, W.J. / Hipgrave Ederveen, A.L. / van Zeijl, L. / Joosten, R.P. / Perrakis, A.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: chem_comp / entity_poly / pdbx_seq_map_depositor_info
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / software / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Jul 30, 2025Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 4.0Aug 26, 2026Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.category / _pdbx_modification_feature.comp_id_linking_atom / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_auth_comp_id / _pdbx_modification_feature.modified_residue_auth_seq_id / _pdbx_modification_feature.modified_residue_id / _pdbx_modification_feature.modified_residue_id_linking_atom / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_modification_feature.modified_residue_label_comp_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_modification_feature.modified_residue_symmetry / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_modification_feature.type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,95815
Polymers95,0381
Non-polymers1,92014
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-31 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.750, 63.450, 70.550
Angle α, β, γ (deg.)99.330, 105.910, 99.510
Int Tables number1
Space group name H-MP1

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD


Mass: 95037.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Non-polymers , 7 types, 167 molecules

#3: Chemical ChemComp-5JK / 7alpha-hydroxycholesterol / (3beta,7alpha,9beta,14beta)-cholest-5-ene-3,7-diol


Mass: 402.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O4V
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Protein buffer: 4.5 mg/ml autotaxin, incubated with 1 mM orthovanadate, 20 mM hepes pH 7.4, 150 mM NaCl Crystallisation condition: 18% (w/v) PEG3350, 0.2 M NH4I, 0.4M NaSCN

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 1, 2010
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 39503 / % possible obs: 90.2 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.4 / % possible all: 90.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefmac_5.8.0135refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dlt

5dlt


Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / Matrix type: sparse / SU B: 18.451 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.359 / ESU R Free: 0.232
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED Zinc and Iodine atoms have anisotropic residual B-factors
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 2000 5.1 %RANDOM
Rwork0.2025 ---
obs0.2043 37463 90.06 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 123.5 Å2 / Biso mean: 42.948 Å2 / Biso min: 16.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å21.84 Å2-0.24 Å2
2---0.47 Å20.89 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 68 154 6559
Biso mean--41.81 38.6 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196596
X-RAY DIFFRACTIONr_bond_other_d0.0010.026037
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9658965
X-RAY DIFFRACTIONr_angle_other_deg0.894313958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90923.175315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.971151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831548
X-RAY DIFFRACTIONr_chiral_restr0.0690.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021564
X-RAY DIFFRACTIONr_mcbond_it1.9622.4133133
X-RAY DIFFRACTIONr_mcbond_other1.9572.4123132
X-RAY DIFFRACTIONr_mcangle_it3.1433.6123911
X-RAY DIFFRACTIONr_sphericity_bonded45.77558
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.2-2.2570.3251500.3242768324589.9230.315
2.257-2.3190.3471490.2992712315990.5670.287
2.319-2.3860.3191340.2782627307189.9060.264
2.386-2.4590.2761240.2752533297189.4310.261
2.459-2.540.2921230.2472496293689.2030.23
2.54-2.6290.2711470.2382277278087.1940.219
2.629-2.7280.2491090.2312272267688.9760.211
2.728-2.8390.2531130.2122171260487.7110.193
2.839-2.9650.2911070.2182090247788.6960.2
2.965-3.110.281990.1882076237191.7330.174
3.11-3.2770.1841070.1761975226691.880.168
3.277-3.4760.2481020.1691835214390.3870.162
3.476-3.7150.188890.1651752203690.4220.164
3.715-4.0120.199830.1641601185890.6350.164
4.012-4.3930.188890.1541453171390.0180.16
4.393-4.9090.194940.1531344156591.8850.163
4.909-5.6630.244690.1971190137491.630.21
5.663-6.9230.295510.2171040116793.4880.227
6.923-9.7370.169460.18180089994.1050.197
9.737-66.2050.22150.21445150692.0950.239
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)
10.53960.1824-0.39560.7454-0.15621.36990.06220.04510.046-0.0020.0325-0.045-0.14310.0859-0.09470.123-0.11380.08970.1265-0.08230.068315.24680.307529.1884
21.8320.01210.0370.97-0.03951.81810.07640.0075-0.46740.0813-0.04960.06770.3578-0.2055-0.02680.2046-0.140.07310.0995-0.07290.1895-7.6402-31.64541.5318
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 540
2X-RAY DIFFRACTION1A1860 - 1864
3X-RAY DIFFRACTION1A1866 - 1868
4X-RAY DIFFRACTION2A541 - 859
5X-RAY DIFFRACTION2A1865
6X-RAY DIFFRACTION2A1869 - 1891

+
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