[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

TitleStructural genomics for drug design against the pathogen Coxiella burnetii.
Journal, issue, pagesProteins, Vol. 83, Page 2124-2136, Year 2015
Publish dateSep 9, 2011 (structure data deposition date)
AuthorsFranklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
External linksProteins / PubMed:26033498
MethodsX-ray diffraction
Resolution1.5 - 3.298 Å
Structure data

PDB-3tq8:
Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with trimethoprim
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3tq9:
Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with methotrexate
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3tqa:
Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with NADPH
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3tqb:
Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with folate
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3tqc:
Structure of the pantothenate kinase (coaA) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3tqd:
Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-3tqe:
Structure of the malonyl CoA-acyl carrier protein transacylase (fabD) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-3tqf:
Structure of the Hpr(Ser) kinase/phosphatase from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-3tqg:
Structure of the 2-methylcitrate synthase (prpC) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3tqh:
Structure of the quinone oxidoreductase from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.44 Å

PDB-3tqi:
Structure of the GMP synthase (guaA) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.84 Å

PDB-3tqj:
Structure of the superoxide dismutase (Fe) (sodB) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.004 Å

PDB-3tql:
Structure of the amino acid ABC transporter, periplasmic amino acid-binding protein from Coxiella burnetii.
Method: X-RAY DIFFRACTION / Resolution: 1.594 Å

PDB-3tqm:
Structure of an ribosomal subunit interface protein from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.45 Å

PDB-3tqn:
Structure of the transcriptional regulator of the GntR family, from Coxiella burnetii.
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-3tqo:
Structure of the cysteinyl-tRNA synthetase (cysS) from Coxiella burnetii.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3tqp:
Structure of an enolase (eno) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-3tqq:
Structure of the methionyl-tRNA formyltransferase (fmt) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-3tqr:
Structure of the phosphoribosylglycinamide formyltransferase (purN) in complex with CHES from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.97 Å

PDB-3tqs:
Structure of the dimethyladenosine transferase (ksgA) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-3tqt:
Structure of the D-alanine-D-alanine ligase from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.88 Å

PDB-3tqu:
Structure of a HAM1 protein from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3tqw:
Structure of a ABC transporter, periplasmic substrate-binding protein from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-3tqx:
Structure of the 2-amino-3-ketobutyrate coenzyme A ligase (kbl) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.304 Å

PDB-3tqy:
Structure of a single-stranded DNA-binding protein (ssb), from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.6001 Å

PDB-3tqz:
Structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase (dut) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-3tr0:
Structure of guanylate kinase (gmk) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.851 Å

PDB-3tr1:
Structure of a 3-phosphoshikimate 1-carboxyvinyltransferase (aroA) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-3tr2:
Structure of a orotidine 5'-phosphate decarboxylase (pyrF) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.001 Å

PDB-3tr3:
Structure of a bolA protein homologue from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.456 Å

PDB-3tr4:
Structure of an inorganic pyrophosphatase (ppa) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-3tr5:
Structure of a peptide chain release factor 3 (prfC) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-3tr6:
Structure of a O-methyltransferase from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.7 Å

PDB-3tr7:
Structure of a uracil-DNA glycosylase (ung) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.1958 Å

PDB-3tr8:
Structure of an oligoribonuclease (orn) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.503 Å

PDB-3tr9:
Structure of a dihydropteroate synthase (folP) in complex with pteroic acid from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.895 Å

PDB-3trb:
Structure of an addiction module antidote protein of a HigA (higA) family from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.001 Å

PDB-3trc:
Structure of the GAF domain from a phosphoenolpyruvate-protein phosphotransferase (ptsP) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-3trd:
Structure of an alpha-beta serine hydrolase homologue from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-3tre:
Structure of a translation elongation factor P (efp) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.899 Å

PDB-3trf:
Structure of a shikimate kinase (aroK) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-3trg:
Structure of an acylphosphatase from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.601 Å

PDB-3trh:
Structure of a phosphoribosylaminoimidazole carboxylase catalytic subunit (purE) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.203 Å

PDB-3tri:
Structure of a pyrroline-5-carboxylate reductase (proC) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3tth:
Structure of the spermidine N1-acetyltransferase (speG) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 3.298 Å

PDB-3ty2:
Structure of a 5'-nucleotidase (surE) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 1.885 Å

PDB-3uwc:
Structure of an aminotransferase (DegT-DnrJ-EryC1-StrS family) from Coxiella burnetii in complex with PMP
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4f3q:
Structure of a YebC family protein (CBU_1566) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-4f3r:
Structure of phosphopantetheine adenylyltransferase (CBU_0288) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-4nbq:
Structure of the polynucleotide phosphorylase (CBU_0852) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.9138 Å

PDB-4ng4:
Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii
Method: X-RAY DIFFRACTION / Resolution: 2.78 Å

Chemicals

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

ChemComp-TOP:
TRIMETHOPRIM / antibiotic*YM / Trimethoprim

ChemComp-HOH:
WATER / Water

ChemComp-MTX:
METHOTREXATE / chemotherapy*YM / Methotrexate

ChemComp-FOL:
FOLIC ACID / Folate

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-NI:
NICKEL (II) ION / Nickel

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-GLY:
GLYCINE / Glycine

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-FE2:
Unknown entry

ChemComp-ARG:
ARGININE / Arginine

ChemComp-IMD:
IMIDAZOLE / Imidazole

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM / CHES (buffer)

ChemComp-CL:
Unknown entry / Chloride

ChemComp-CA:
Unknown entry

ChemComp-MET:
METHIONINE / Methionine

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE / Pyridoxal phosphate

ChemComp-5GP:
GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate

ChemComp-CO:
Unknown entry

ChemComp-MN:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

ChemComp-PT1:
PTEROIC ACID

ChemComp-NA:
Unknown entry

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Tris

ChemComp-DIO:
1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane

ChemComp-PMP:
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

Source
  • coxiella burnetii (bacteria)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / dihydrofolate reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / OXIDOREDUCTASE / TRANSFERASE / Biosynthesis of cofactors / prosthetic groups / carriers / Cell envelope / Fatty acid/phospholipid metabolism / HYDROLASE / Energy metabolism / quinone oxidoreductase / LIGASE / GMP synthase / superoxide dismutase (Fe) / TRANSPORT PROTEIN / Transport and binding proteins / PROTEIN BINDING / Protein synthesis / TRANSCRIPTION / Regulatory functions / LYASE / Purines / pyrimidines / nucleosides / nucleotides / HAM1 protein / DNA replication / Amino acid biosynthesis / UNKNOWN FUNCTION / Cellular processes / stress-induced / Central intermediary metabolism / TRANSLATION / DNA metabolism / and carriers / DNA BINDING PROTEIN / Mobile and extrachromosomal element functions / Signal transduction / Fatty acid and phospholipid metabolism / survival protein / phosphatase / lipopolysaccharide biosynthesis / YebC family / phosphopantetheine adenylyltranferase / Phosphorylase / phosphoglycerate kinase

+
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