[English] 日本語
Yorodumi
- PDB-8oll: Staphylococcus aureus ClpP in complex with the natural product be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8oll
TitleStaphylococcus aureus ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.7 A resolution
ComponentsATP-dependent Clp protease proteolytic subunit
KeywordsHYDROLASE / anti-virulence / caseinolytic protease / inhibitor / natural product / mode of action
Function / homology
Function and homology information


endopeptidase Clp / ATP-dependent peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
Cystargolide A (bound) / ATP-dependent Clp protease proteolytic subunit
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsIlligmann, A. / Vielberg, M.-T. / Lakemeyer, M. / Wolf, F. / Staudt, N. / Dema, T. / Stange, P. / Malik, I. / Grond, S. / Sieber, S.A. ...Illigmann, A. / Vielberg, M.-T. / Lakemeyer, M. / Wolf, F. / Staudt, N. / Dema, T. / Stange, P. / Malik, I. / Grond, S. / Sieber, S.A. / Groll, M. / Kaysser, L. / Broetz-Oesterhelt, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FB 1035 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A.
Authors: Illigmann, A. / Vielberg, M.T. / Lakemeyer, M. / Wolf, F. / Dema, T. / Stange, P. / Kuttenlochner, W. / Liebhart, E. / Kulik, A. / Staudt, N.D. / Malik, I. / Grond, S. / Sieber, S.A. / ...Authors: Illigmann, A. / Vielberg, M.T. / Lakemeyer, M. / Wolf, F. / Dema, T. / Stange, P. / Kuttenlochner, W. / Liebhart, E. / Kulik, A. / Staudt, N.D. / Malik, I. / Grond, S. / Sieber, S.A. / Kaysser, L. / Groll, M. / Brotz-Oesterhelt, H.
History
DepositionMar 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)642,63256
Polymers632,20328
Non-polymers10,42928
Water5,098283
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,31628
Polymers316,10214
Non-polymers5,21414
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area55960 Å2
ΔGint-210 kcal/mol
Surface area93500 Å2
MethodPISA
2
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)321,31628
Polymers316,10214
Non-polymers5,21414
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54000 Å2
ΔGint-205 kcal/mol
Surface area91970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.410, 109.730, 173.610
Angle α, β, γ (deg.)110.09, 89.44, 108.80
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein ...
ATP-dependent Clp protease proteolytic subunit / / Endopeptidase Clp


Mass: 22578.680 Da / Num. of mol.: 28
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAR0823 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6GIM3, endopeptidase Clp
#2: Chemical...
ChemComp-VSZ / Cystargolide A (bound) / (2S,3S)-2-[[(2S)-2-[[(2R,3S)-3-methanoyl-4-methyl-2-oxidanyl-pentanoyl]amino]-3-methyl-butanoyl]amino]-3-methyl-pentanoic acid


Mass: 372.456 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C18H32N2O6 / Source: (synth.) synthetic construct (others) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium citrate, 20% PEG3350 / PH range: 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 157322 / % possible obs: 91 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16383 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 40.286 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25827 7862 5 %RANDOM
Rwork0.22438 ---
obs0.23116 149373 91.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å2-1.72 Å2-1.93 Å2
2---1.84 Å23.64 Å2
3---2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39781 0 728 285 40794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01941014
X-RAY DIFFRACTIONr_bond_other_d0.0040.0239272
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.98955415
X-RAY DIFFRACTIONr_angle_other_deg1.2273.00891192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.48255102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24425.5431804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.079157374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.65115206
X-RAY DIFFRACTIONr_chiral_restr0.0550.26543
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02145067
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027355
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1347.58520570
X-RAY DIFFRACTIONr_mcbond_other1.1347.58520569
X-RAY DIFFRACTIONr_mcangle_it1.44211.35825618
X-RAY DIFFRACTIONr_mcangle_other1.44211.35925619
X-RAY DIFFRACTIONr_scbond_it0.9627.7220444
X-RAY DIFFRACTIONr_scbond_other0.9627.7220445
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.41511.53829798
X-RAY DIFFRACTIONr_long_range_B_refined2.0337.72161126
X-RAY DIFFRACTIONr_long_range_B_other1.9727.72161076
X-RAY DIFFRACTIONr_rigid_bond_restr1.787380286
X-RAY DIFFRACTIONr_sphericity_free85.2965192
X-RAY DIFFRACTIONr_sphericity_bonded24.18579874
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 584 -
Rwork0.348 11092 -
obs--91.86 %
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)
10.03820.03480.02370.07080.0120.01830.00010.0041-0.00050.003-0.0097-0.0226-0.0041-0.00180.00960.10620.01670.0350.1519-0.02490.0486-6.203649.1903-51.1225
20.0026-0.00360.00210.109-0.02450.0118-0.0118-0.00790.00120.02240.0047-0.0073-0.0046-0.01450.00710.10590.02140.03910.1537-0.03480.0365-17.119241.4146-29.0989
30.0899-0.00780.00210.0923-0.00730.0021-0.0107-0.00210.02670.03460.0069-0.00210.009-0.00470.00380.12270.02260.02910.1501-0.04560.0345-6.172733.1967-7.3015
40.01080.0164-0.01090.042-0.02340.0141-0.0013-0.00520.00530.0192-0.0012-0.0103-0.0037-0.00280.00260.12910.0230.01410.1409-0.04960.044919.263130.168-1.8306
50.0273-0.01780.03940.0745-0.00490.0758-0.01230.00010.0150.01810.0079-0.0109-0.0049-0.00730.00450.11570.01840.01620.1441-0.03260.066541.206433.4578-17.6419
60.0148-0.0030.0020.0123-0.01650.0313-0.00750.0020.00520.0086-0.0029-0.0189-0.00730.00180.01040.1050.0160.02530.1497-0.02360.078740.267342.7838-42.96
70.0727-0.01410.02990.0285-0.0210.0438-0.00940.00770.02060.0081-0.0104-0.0274-0.00080.00980.01980.10440.020.03940.1544-0.02260.062118.923949.625-57.5925
80.07660.02180.01920.0460.04550.0479-0.00810.0035-0.0003-0.00350.0067-0.0083-0.0050.00220.00140.11750.01870.02820.1464-0.03240.045936.3724-11.4253-31.0794
90.0898-0.0473-0.03290.02870.01240.025-0.00230.00020.00270.00580.0103-0.00290.0062-0.0043-0.0080.12140.01630.0280.1468-0.03650.035314.7702-15.0742-17.1346
100.0901-0.03160.04490.0119-0.01590.0234-0.00340.00490.0002-0-0.0006-0.00310.0023-0.00820.0040.11480.01630.04560.1523-0.03240.0343-10.0568-11.4479-24.9129
110.00190.0013-0.00690.1554-0.04840.03920.0030.00380.0015-0.00850.00250.01310.0037-0.0047-0.00550.1110.01420.03010.153-0.03160.0366-19.599-2.8742-47.8401
120.02320.00070.00170.11860.03940.01410.00460.0196-0.008-0.0142-0.00770.00020.00550.0010.00310.11690.01680.0360.1545-0.03830.0243-6.354.3242-69.1869
130.0205-0.01220.01440.1155-0.03020.04510.01670.02140.0070.0001-0.00930.00070.0220.007-0.00740.10720.02220.04950.1574-0.03540.042620.11834.7752-72.695
140.07530.0185-0.01570.01860.00850.0171-0.00780.00920.0015-0.00680.0072-0.0073-0.00310.00440.00070.10830.01930.03910.1483-0.03230.050339.0827-2.5008-55.5344
150.0136-0.02290.0250.0398-0.04490.05210.01220.00540.0022-0.0078-0.0165-0.00050.00760.04170.00430.09210.02240.05320.1773-0.02270.0381-3.8785-22.193623.3618
160.03750.01730.02810.02020.03440.0616-0.0023-0.0036-0.0083-0.01190.0054-0.0032-0.00620.0186-0.00310.11350.01950.04050.1524-0.03060.0351-3.9583-34.100147.1897
170.0795-0.02140.02120.0064-0.00560.04390.0115-0.0186-0.0284-0.00430.01340.00480.0171-0.0099-0.02490.10980.01330.0340.1504-0.02030.0457-24.1159-45.622159.9648
180.0941-0.0553-0.05370.05220.00620.06830.0154-0.0048-0.0151-0.0303-0.00340.03240.0321-0.0075-0.0120.095-0.00190.02630.1627-0.00360.0699-49.6944-47.923552.6944
190.0314-0.04520.02510.0907-0.03340.02350.01080.0142-0.01960.00840.01370.0087-00.0005-0.02450.10710.01230.02950.1501-0.0120.0636-60.8146-39.668329.9128
200.0193-0.0359-0.00110.1464-0.00590.00430.0020.0008-0.0099-0.02140.00650.01820.00350.0036-0.00850.11350.01030.02820.1504-0.02730.04-49.525-26.81469.5034
210.05040.00720.05970.1793-0.01570.08050.0158-0.00120.0033-0.0135-0.00520.01840.01840.028-0.01060.10960.01440.04720.1567-0.01980.0291-24.2952-18.88656.5717
220.05940.01010.08150.3617-0.05440.1386-0.0294-0.0385-0.01880.01260.03920.0141-0.0228-0.0426-0.00980.05770.02290.05330.1791-0.01790.0587-71.1163-0.343352.9233
230.0102-0.0177-0.0060.06560.0430.0341-0.0152-0.0318-0.00750.00210.02160.0044-0.0165-0.0093-0.00640.08960.01720.06060.1843-0.01290.0448-57.1567-6.966674.4146
240.0108-0.03030.01040.13850.00320.0345-0.0058-0.0107-0.0010.01340.01110.0062-0.00870.0031-0.00530.11380.01690.03890.1593-0.03210.0226-31.5453-3.300779.9173
250.02330.0135-0.00080.0385-0.0340.0392-0.0144-0.00040.01040.0067-0.0031-0.0053-0.00070.00770.01750.11860.0140.02690.1474-0.03320.0347-12.74568.619465.0208
260.011-0.00340.01290.0016-0.00570.0358-0.00840.00210.0068-0.00150.0027-0.0054-0.01180.01640.00570.12220.00810.0250.1548-0.02760.0485-15.401719.84440.9475
270.09030.0366-0.00350.0329-0.01310.0082-0.00930.0086-0.00120.0097-0-0.0109-0.0119-0.00550.00930.12840.0150.02690.149-0.03070.0272-37.5621.839426.0036
280.0443-0.00380.0420.14360.04430.0592-0.0237-0.01540.0062-0.00010.00280.0222-0.0079-0.00760.0210.09660.01760.03320.1511-0.03270.038-62.089412.945131.4166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 193
2X-RAY DIFFRACTION2B1 - 193
3X-RAY DIFFRACTION3C2 - 193
4X-RAY DIFFRACTION4D3 - 193
5X-RAY DIFFRACTION5E18 - 192
6X-RAY DIFFRACTION6F4 - 193
7X-RAY DIFFRACTION7G4 - 193
8X-RAY DIFFRACTION8H3 - 193
9X-RAY DIFFRACTION9I2 - 195
10X-RAY DIFFRACTION10J2 - 193
11X-RAY DIFFRACTION11K3 - 192
12X-RAY DIFFRACTION12L3 - 193
13X-RAY DIFFRACTION13M3 - 192
14X-RAY DIFFRACTION14N4 - 193
15X-RAY DIFFRACTION15O4 - 193
16X-RAY DIFFRACTION16P3 - 193
17X-RAY DIFFRACTION17Q3 - 193
18X-RAY DIFFRACTION18R3 - 193
19X-RAY DIFFRACTION19S4 - 193
20X-RAY DIFFRACTION20T4 - 193
21X-RAY DIFFRACTION21U4 - 193
22X-RAY DIFFRACTION22V4 - 192
23X-RAY DIFFRACTION23W3 - 193
24X-RAY DIFFRACTION24X3 - 193
25X-RAY DIFFRACTION25Y4 - 192
26X-RAY DIFFRACTION26Z4 - 193
27X-RAY DIFFRACTION27a4 - 193
28X-RAY DIFFRACTION28b3 - 192

+
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