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Structure paper

TitleInterplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.
Journal, issue, pagesInt. J. Biol. Macromol., Vol. 262, Page 130041-130041, Year 2024
Publish dateAug 26, 2022 (structure data deposition date)
AuthorsShi, X. / Dai, Y. / Lan, Z. / Wang, S. / Cui, L. / Xiao, C. / Zhao, K. / Li, X. / Liu, W. / Zhang, Q.
External linksInt. J. Biol. Macromol. / PubMed:38336327
MethodsX-ray diffraction
Resolution1.4 - 1.89 Å
Structure data

PDB-8gpc:
Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed ampicillin
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-8gpd:
Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin V
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-8gpe:
Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed penicillin G
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-8i8f:
Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-ZZ7:
(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-JXF:
(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-phenoxyethanoylamino)ethyl]-1,3-thiazolidine-4-carboxylic acid

ChemComp-K:
Unknown entry

ChemComp-PNK:
(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / antibiotic*YM


ChemComp, No image

ChemComp-OL6:
Unknown entry

Source
  • klebsiella pneumoniae (bacteria)
KeywordsHYDROLASE / HYDROLASE-INHIBITOR / penicillin / hydrolase-inhibitor complex

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