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Structure paper

TitleNon-classical transpeptidases yield insight into new antibacterials.
Journal, issue, pagesNat. Chem. Biol., Vol. 13, Page 54-61, Year 2017
Publish dateSep 18, 2015 (structure data deposition date)
AuthorsKumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. ...Kumar, P. / Kaushik, A. / Lloyd, E.P. / Li, S.G. / Mattoo, R. / Ammerman, N.C. / Bell, D.T. / Perryman, A.L. / Zandi, T.A. / Ekins, S. / Ginell, S.L. / Townsend, C.A. / Freundlich, J.S. / Lamichhane, G.
External linksNat. Chem. Biol. / PubMed:27820797
MethodsX-ray diffraction
Resolution1.79 - 2.25 Å
Structure data

PDB-5du7:
Crystal structure of ldtMt2 at 1.79 Angstrom resolution
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

PDB-5duj:
Crystal structure of ldtMt2 in complex with Faropenem adduct
Method: X-RAY DIFFRACTION / Resolution: 2.17 Å

PDB-5dvp:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with Doripenem adduct
Method: X-RAY DIFFRACTION / Resolution: 2.18 Å

PDB-5dzj:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation A
Method: X-RAY DIFFRACTION / Resolution: 2.095 Å

PDB-5dzp:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T206 in conformation B
Method: X-RAY DIFFRACTION / Resolution: 2.19 Å

PDB-5e1g:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T208
Method: X-RAY DIFFRACTION / Resolution: 1.852 Å

PDB-5e1i:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T210
Method: X-RAY DIFFRACTION / Resolution: 2.003 Å

PDB-5e51:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 with Faropenem adduct
Method: X-RAY DIFFRACTION / Resolution: 2.25 Å

PDB-5e5l:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 1 at 1.89 Angstrom
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-5k69:
Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase 2 with carbapenem drug T224
Method: X-RAY DIFFRACTION / Resolution: 2.001 Å

Chemicals

ChemComp-HOH:
WATER / Water

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-BME:
BETA-MERCAPTOETHANOL / 2-Mercaptoethanol

ChemComp-DGF:
(2R,5R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-[(2R)-tetrahydrofuran-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid

ChemComp-DRW:
(2S,3R,4S)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid

ChemComp-POA:
PHOSPHONOACETALDEHYDE

ChemComp-6B7:
(2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid

ChemComp-T8G:
(2~{S},3~{R},4~{R})-4-(2-cyclohexyloxy-2-oxidanylidene-ethyl)sulfanyl-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid

ChemComp-NA:
Unknown entry

ChemComp-6B8:
(2S,3R,4R)-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-4-(methylsulfanyl)-3,4-dihydro-2H-pyrrole-5-carboxylic acid

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-5KO:
(3R)-3-hydroxybutanal

ChemComp-6QR:
(2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid

Source
  • mycobacterium tuberculosis (bacteria)
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
  • mycobacterium tuberculosis (strain cdc 1551 / oshkosh) (bacteria)
KeywordsTRANSFERASE / Peptidoglycan synthesis enzyme / cell wall enzyme / LD-TRANSPEPTIDASE / L / D-transpeptidase 1 / ldtMt1 / Mycobacterium tuberculosis / TRANSFERASE/TRANSFERASE INHIBITOR / peptidase / IgD_like domain / YkuD domain / TRANSFERASE-TRANSFERASE INHIBITOR complex

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