[English] 日本語
Yorodumi
- PDB-7q24: Crystal structure of Angiotensin-1 converting enzyme N-domain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q24
TitleCrystal structure of Angiotensin-1 converting enzyme N-domain in complex with dual ACE/NEP inhibitor AD011
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / Angiotensin-1 converting enzyme / Dual inhibitor / NEP / Metalloprotease
Function / homology
Function and homology information


mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / tripeptidyl-peptidase activity / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / regulation of renal output by angiotensin / positive regulation of peptidyl-cysteine S-nitrosylation ...mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / tripeptidyl-peptidase activity / exopeptidase activity / regulation of angiotensin metabolic process / substance P catabolic process / peptidyl-dipeptidase A / regulation of renal output by angiotensin / positive regulation of peptidyl-cysteine S-nitrosylation / negative regulation of calcium ion import / response to laminar fluid shear stress / positive regulation of systemic arterial blood pressure / negative regulation of gap junction assembly / metallodipeptidase activity / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / negative regulation of D-glucose import / vasoconstriction / neutrophil mediated immunity / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / hormone metabolic process / antigen processing and presentation of peptide antigen via MHC class I / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / heterocyclic compound binding / lung alveolus development / arachidonate secretion / post-transcriptional regulation of gene expression / eating behavior / peptide catabolic process / heart contraction / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / blood vessel remodeling / hematopoietic stem cell differentiation / regulation of vasoconstriction / peptidyl-dipeptidase activity / animal organ regeneration / amyloid-beta metabolic process / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / positive regulation of vasoconstriction / carboxypeptidase activity / sperm midpiece / blood vessel diameter maintenance / basal plasma membrane / response to nutrient levels / kidney development / angiotensin-activated signaling pathway / female pregnancy / cellular response to glucose stimulus / brush border membrane / regulation of synaptic plasticity / metalloendopeptidase activity / regulation of blood pressure / male gonad development / metallopeptidase activity / peptidase activity / actin binding / spermatogenesis / endopeptidase activity / response to lipopolysaccharide / lysosome / response to hypoxia / calmodulin binding / endosome / positive regulation of apoptotic process / response to xenobiotic stimulus / external side of plasma membrane / negative regulation of gene expression / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Chem-8KC / ACETATE ION / DI(HYDROXYETHYL)ETHER / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCozier, G.E. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M026647/1 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Probing the Requirements for Dual Angiotensin-Converting Enzyme C-Domain Selective/Neprilysin Inhibition.
Authors: Arendse, L.B. / Cozier, G.E. / Eyermann, C.J. / Basarab, G.S. / Schwager, S.L. / Chibale, K. / Acharya, K.R. / Sturrock, E.D.
History
DepositionOct 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,11531
Polymers145,2132
Non-polymers5,90229
Water9,188510
1
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,84616
Polymers72,6071
Non-polymers3,23915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,26915
Polymers72,6071
Non-polymers2,66314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.766, 77.608, 81.647
Angle α, β, γ (deg.)88.931, 64.553, 75.009
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Angiotensin-converting enzyme / ACE / Dipeptidyl carboxypeptidase I / Kininase II


Mass: 72606.508 Da / Num. of mol.: 2
Mutation: N9Q, N25Q, N82Q, N117Q, N131Q, N289Q, Q545R, P576L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE, DCP, DCP1 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A

-
Sugars , 4 types, 6 molecules

#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
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#15: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 11 types, 533 molecules

#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-8KC / (2~{S})-2-[[(2~{S})-1-[[(2~{S})-3-(1~{H}-indol-3-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-hexan-2-yl]amino]-4-phenyl-butanoic acid


Mass: 479.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N3O5 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent cations, 30% PEG550MME/PEG20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2→73.31 Å / Num. obs: 102179 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 30.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.064 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4951 / CC1/2: 0.418 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F9V

6f9v


Resolution: 2→63.12 Å / SU ML: 0.2689 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.4812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2139 1962 1.92 %
Rwork0.1851 100051 -
obs0.1857 102013 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.95 Å2
Refinement stepCycle: LAST / Resolution: 2→63.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 387 510 10824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002210766
X-RAY DIFFRACTIONf_angle_d0.53714636
X-RAY DIFFRACTIONf_chiral_restr0.03521535
X-RAY DIFFRACTIONf_plane_restr0.00421883
X-RAY DIFFRACTIONf_dihedral_angle_d14.73073955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.40991350.34737093X-RAY DIFFRACTION96.51
2.05-2.110.29181160.30487157X-RAY DIFFRACTION96.97
2.11-2.170.32961400.27157074X-RAY DIFFRACTION96.66
2.17-2.240.28121410.24887141X-RAY DIFFRACTION96.98
2.24-2.320.25361230.23237063X-RAY DIFFRACTION96.83
2.32-2.410.24971310.21847174X-RAY DIFFRACTION97.01
2.41-2.520.25011550.20247091X-RAY DIFFRACTION97.13
2.52-2.650.2031350.19027137X-RAY DIFFRACTION97.26
2.65-2.820.20711620.18847107X-RAY DIFFRACTION97.58
2.82-3.040.20111420.18317214X-RAY DIFFRACTION98.03
3.04-3.340.21491440.18297187X-RAY DIFFRACTION98.13
3.34-3.830.20171340.16087232X-RAY DIFFRACTION98.41
3.83-4.820.18281580.13437204X-RAY DIFFRACTION98.17
4.82-63.120.17031460.15967177X-RAY DIFFRACTION98.28
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)
13.490156418711.62305025784-1.217878197252.03584132407-0.9125487605561.900468084610.195037947669-0.142080527382-1.03014863983-0.214617945407-0.3048350844350.2536662592620.238900483167-0.1488088309440.1022164212820.2314194383820.0168948152048-0.1185074877060.376281762716-0.02531696822730.730801839107-76.110507689152.5391066578-19.1226793282
22.378997462970.1346866222890.03112555768041.129431205290.04253820320441.06718159150.2433680130310.0334045739057-0.189114096331-0.125411429027-0.1040096523840.1476316635430.0152736013355-0.0334526328279-0.1733240092580.2406518953810.0449448916541-0.0630741034320.2587779313230.02762684218870.283604777159-66.130788440166.498949159-19.0418372244
32.80537752458-0.261752092597-0.1211731208991.13677970197-0.07590646059150.5198522509090.08605359538720.04503014502750.085015673553-0.0685411969821-0.0488991757244-0.113295075432-0.05633483933840.0690630055947-0.01719442890770.220971992561-0.01401521634710.04011599757320.197485772908-0.002289848191730.173506894471-44.058280528572.4690080479-11.1351335377
43.60213628932-1.07603591201-0.2754832024572.253046696870.179456904591.633006336480.2722032649250.4528064898660.0538099219077-0.222054917976-0.182705539736-0.0285172091877-0.162765438409-0.0650980898414-0.1029112700710.3132943789840.07555971167150.03362119195360.354559540762-0.01891232582080.23064412012-47.611619081954.9991055693-31.0345290905
53.09804583831-0.476914557348-0.5621859743931.940451030450.04910907495291.970745676490.1217948592620.15488948011-0.15950071677-0.191651710686-0.0842737276571-0.0821730578142-0.0457047647263-0.0712848538322-0.02930077835940.2165830222420.02705793093310.004749007896760.188490344649-0.02509205790210.196035900378-47.443207467652.5911429542-21.2477258152
62.07006212927-1.157327648360.02879327482792.054997814990.02796248174220.4873475044730.09212905499510.06141641768430.072851127509-0.0556112940809-0.0462409175095-0.163101328372-0.06599101473790.0586520472131-0.03689621261270.196463615383-0.01285823504760.02035896167770.2037515587240.02356827008480.168841384259-47.22681331273.5847973808-10.0254592347
71.274818214320.5627570430850.1069266528192.827609506890.7575587907690.542527783475-0.00659591100954-0.0267093029646-0.1542062496950.1200014344610.127413326971-0.2104302879150.04691272916110.11450410743-0.1203099150130.1982321510380.0193433765621-0.006017648666220.2475751507080.03832122704850.195197270228-39.748831935257.7638062259-7.85820598787
81.749240312031.25315190141-1.677927906654.05727949876-1.34826274982.38850025453-0.325788358967-0.204666896956-0.1676105032170.5121080762480.2215964802580.2881223691040.7087628867830.03758950866480.1089794628070.855463963380.2273186831840.1180968466330.4989332763550.06238324736840.405608558373-50.616614161974.459961105539.4842648382
91.58889823497-0.740251717358-0.5563993782282.09532835015-0.1575557421863.09858384577-0.132514765544-0.2628001082240.09599099179070.3269062294870.247692474247-0.4756760450390.0622784956360.6369842249230.06987957991820.2478797795010.0277817783257-0.02889859905650.377650994324-0.08782562344540.327622260125-37.110900857291.985439384718.4190816165
100.989907721239-0.546334050729-0.6806445561611.541887446841.370919444122.32000852189-0.00159171294019-0.0271185157240.02277433321560.100747011903-0.05399185072570.151968758663-0.096479934737-0.1988763013830.01060730105050.265659645976-0.001634644329310.04223670774110.187060812080.02995582056040.260427551882-57.615950484197.735436484518.0194335987
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )AA1 - 431 - 43
22chain 'A' and (resid 44 through 152 )AA44 - 15244 - 149
33chain 'A' and (resid 153 through 279 )AA153 - 279150 - 276
44chain 'A' and (resid 280 through 336 )AA280 - 336277 - 333
55chain 'A' and (resid 337 through 417 )AA337 - 417334 - 414
66chain 'A' and (resid 418 through 498 )AA418 - 498415 - 495
77chain 'A' and (resid 499 through 609 )AA499 - 609496 - 606
88chain 'B' and (resid 1 through 104 )BS1 - 1041 - 104
99chain 'B' and (resid 105 through 189 )BS105 - 189105 - 189
1010chain 'B' and (resid 190 through 609 )BS190 - 609190 - 609

+
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