[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitlePanDDA analysis group deposition
Journal, issue, pagesChemrxiv, Year 2023
Publish dateMay 30, 2022 (structure data deposition date)
AuthorsGeorgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R.
External linksChemrxiv / Search PubMed
MethodsX-ray diffraction
Resolution1.49 - 2.38 Å
Structure data

PDB-5sn5:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2856434897
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-5sn6:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2856434942
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-5sn7:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z32327641
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-5sn8:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z375990520
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-5sn9:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z57258487
Method: X-RAY DIFFRACTION / Resolution: 1.58 Å

PDB-5sna:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z30620520
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-5snb:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1545313172
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-5snc:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z768399682
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-5snd:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1217960891
Method: X-RAY DIFFRACTION / Resolution: 1.69 Å

PDB-5sne:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z192955056
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-5snf:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z87615031
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-5sng:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z383325512
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-5snh:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z198194394
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-5sni:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z285782452
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-5snj:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z906021418
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-5snk:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2856434941
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-5snl:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2027049478
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-5snm:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z135439900
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-5snn:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1954800564
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-5sno:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z364368134
Method: X-RAY DIFFRACTION / Resolution: 1.86 Å

PDB-5snp:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z381729066
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-5snq:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1891773476
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-5snr:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z198195770
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-5sns:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1354416068
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-5snt:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z30820160
Method: X-RAY DIFFRACTION / Resolution: 2.16 Å

PDB-5snu:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2856434770
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-5snv:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z295848548
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-5snw:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z730649594
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-5snx:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1267881672
Method: X-RAY DIFFRACTION / Resolution: 1.99 Å

PDB-5sny:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1827602749
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-5snz:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z44567722
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-5so0:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z24758179
Method: X-RAY DIFFRACTION / Resolution: 2.28 Å

PDB-5so1:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z30620520
Method: X-RAY DIFFRACTION / Resolution: 2.07 Å

PDB-5so2:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z31504642
Method: X-RAY DIFFRACTION / Resolution: 2.38 Å

PDB-5so3:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with JKH100B
Method: X-RAY DIFFRACTION / Resolution: 1.49 Å

PDB-5so4:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with JKH93A
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-5so5:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with JKH93B
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-5so6:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z26968795
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-5so7:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z219104216
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-5so8:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z85895198
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-5so9:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1622626423
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-5soa:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1613492358
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-5sob:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z2204875953
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

PDB-5soc:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1530301542
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-5sod:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1730522163
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-5soe:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z1429867185
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-5sof:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z373768900
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-5sog:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z57328997
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-5soh:
PanDDA analysis group deposition -- Crystal Structure of Pseudomonas Aeruginosa FabF-C164Q mutant protein in complex with Z31432226
Method: X-RAY DIFFRACTION / Resolution: 1.61 Å

Chemicals

ChemComp-Q40:
1-(2-phenylethyl)piperidine-4-carboxamide

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

ChemComp-EJQ:
~{N}-(4-fluorophenyl)-2-pyrrolidin-1-yl-ethanamide

ChemComp-JMM:
[4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone

ChemComp-K0Y:
methyl N-(5-methyl-1,2-oxazole-3-carbonyl)glycinate

ChemComp-NVD:
N-{[4-(dimethylamino)phenyl]methyl}-4H-1,2,4-triazol-4-amine

ChemComp-GX4:
cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone

ChemComp-LWA:
(2~{S})-~{N}-(4-aminocarbonylphenyl)oxolane-2-carboxamide

ChemComp-K0D:
[(2R,5S)-2,5-dimethylmorpholin-4-yl](1,2,5-thiadiazol-3-yl)methanone

ChemComp-Q49:
(3S)-3-(3-fluorophenoxy)-1-methylpyrrolidin-2-one

ChemComp-Q4L:
methyl 4-(4-fluorophenyl)piperazine-1-carboxylate

ChemComp-UQM:
N-[4-(2-amino-2-oxoethyl)phenyl]acetamide

ChemComp-UV7:
N-[(1H-pyrazol-4-yl)methyl]acetamide

ChemComp-O1M:
4-(4-fluorophenyl)piperazine-1-carboxamide

ChemComp-UVA:
N-methyl-2-(methylsulfonyl)aniline

ChemComp-K2G:
5-chloro-2-(propan-2-yl)pyrimidine-4-carboxamide

ChemComp-GOV:
(2S)-1-{[(2H-1,3-benzodioxol-5-yl)methyl]amino}propan-2-ol

ChemComp-K34:
5-(1,3-thiazol-2-yl)-1H-1,2,4-triazole

ChemComp-Q4U:
N,N-diethyl-3-methyl-1,2-oxazole-5-carboxamide

ChemComp-NZ1:
5-methoxy-1,3-benzothiazol-2-amine

ChemComp-Q5H:
3-acetamido-2-methylbenzoic acid

ChemComp-Q5L:
N-(propan-2-yl)-1H-pyrazole-3-carboxamide

ChemComp-Q5U:
1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-yl]-N-methylmethanamine

ChemComp-LJA:
N-[3-(carbamoylamino)phenyl]acetamide

ChemComp-X1J:
1-(5-amino-2H-isoindol-2-yl)ethan-1-one

ChemComp-JFP:
N-(4-methyl-1,3-thiazol-2-yl)propanamide

ChemComp-JFJ:
1-(3-chlorophenyl)-N-methylmethanamine

ChemComp-X0G:
4-[(3-cyclopropyl-1,2,4-oxadiazol-5-yl)methyl]morpholine

ChemComp-NUM:
N-[2-(4-hydroxyphenyl)ethyl]pyridine-2-carboxamide

ChemComp-WN4:
N-(6-methylpyridin-2-yl)-L-prolinamide

ChemComp-K04:
(2S,3S)-3-methyl-N-(1,2,3-thiadiazol-5-yl)tetrahydrofuran-2-carboxamide (non-preferred name)

ChemComp-K0V:
methyl 1-(tert-butylcarbamoyl)piperidine-4-carboxylate

ChemComp-6SU:
methyl 3-(methylsulfonylamino)benzoate

ChemComp-WJD:
2-methoxy-N-phenylacetamide

ChemComp-Q63:
ethyl (2R,3S)-2-fluoro-3-hydroxy-3-(5-methyl-1,2-oxazol-3-yl)propanoate

ChemComp-Q4K:
ethyl (2~{S},3~{R})-3-(5-bromanylpyridin-2-yl)-2-fluoranyl-3-oxidanyl-propanoate

ChemComp-Q6C:
ethyl (2R,3S)-3-(4-chloropyridin-2-yl)-2-fluoro-3-hydroxypropanoate

ChemComp-Q6O:
N-(4-chloro-2,5-dimethoxyphenyl)acetamide

ChemComp-RZS:
6-(ethylamino)pyridine-3-carbonitrile

ChemComp-Q6X:
N-(4-fluorobenzoyl)-N-methylglycine

ChemComp-Q76:
N-[3-(trifluoromethyl)-1H-pyrazol-5-yl]-L-alaninamide

ChemComp-Q7E:
(2R)-4-(1H-pyrazol-1-yl)butan-2-ol

ChemComp-Q7L:
(3P)-3-(2H-1,3-benzodioxol-5-yl)-1H-pyrazole

ChemComp-ZQA:
4-ethyl-2-(1H-imidazol-5-yl)-1,3-thiazole

ChemComp-Q7X:
1-[(2R)-8-fluoro-2-methyl-2,3-dihydro-4H-1,4-benzoxazin-4-yl]ethan-1-one

ChemComp-VVP:
4-methoxy-1H-indole

ChemComp-NUA:
N-(1-ethyl-1H-pyrazol-4-yl)cyclobutanecarboxamide

ChemComp-S2Y:
~{N}-[(4-fluorophenyl)methyl]-4-methoxy-aniline

ChemComp-JGP:
(azepan-1-yl)(2H-1,3-benzodioxol-5-yl)methanone

Source
  • pseudomonas aeruginosa (bacteria)
KeywordsTRANSFERASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / FabF / beta-ketoacyl-acyl-carrier-protein synthase II

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more