6B1F Hydrolase Hydrolase Inhibitor date Sep 18, 2017
title Crystal Structure Kpc-2 Beta-Lactamase Complexed With Wck 42 Soaking
authors F.Van Den Akker, N.Q.Nguyen
compound source
Molecule: Carbapenem-Hydrolyzing Beta-Lactamase Kpc
Chain: A, B
Synonym: Carbapenem-Hydrolyzing Beta-Lactamase Kpc-1
Ec: 3.5.2.6
Engineered: Yes
Organism_scientific: Klebsiella Pneumoniae
Organism_taxid: 573
Gene: Bla, Kpc, Kpc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.150 R_Free 0.174
crystal
cell
length a length b length c angle alpha angle beta angle gamma
34.540 37.432 82.339 92.33 90.05 95.25
method X-Ray Diffractionresolution 1.44 Å
ligand C8Y, CIT, EDO enzyme Hydrolase E.C.3.5.2.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStrategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234., Papp-Wallace KM, Nguyen NQ, Jacobs MR, Bethel CR, Barnes MD, Kumar V, Bajaksouzian S, Rudin SD, Rather PN, Bhavsar S, Ravikumar T, Deshpande PK, Patil V, Yeole R, Bhagwat SS, Patel MV, van den Akker F, Bonomo RA, J Med Chem. 2018 May 10;61(9):4067-4086. doi: 10.1021/acs.jmedchem.8b00091. Epub , 2018 Apr 20. PMID:29627985
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (6b1f.pdb1.gz) 48 Kb
  • Biological Unit Coordinates (6b1f.pdb2.gz) 48 Kb
  • LPC: Ligand-Protein Contacts for 6B1F
  • CSU: Contacts of Structural Units for 6B1F
  • Structure Factors (1905 Kb)
  • Retrieve 6B1F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6B1F from S2C, [Save to disk]
  • View 6B1F in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6B1F
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6b1f_A] [6b1f_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6B1F
  • Community annotation for 6B1F at PDBWiki (http://pdbwiki.org)

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