3S0Z Hydrolase date May 13, 2011
title Crystal Structure Of New Delhi Metallo-Beta-Lactamase (Ndm-1
authors Y.Guo, J.Wang, G.J.Niu, W.Q.Shui, Y.N.Sun, Z.Y.Lou, Z.H.Rao
compound source
Molecule: Metallo-Beta-Lactamase
Chain: A, B
Fragment: Unp Residues 47-270
Synonym: New Delhi Metallo-Beta-Lactamase, Ndm-1
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Blandm-1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31
R_factor 0.234 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.696 40.696 215.292 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand ZN enzyme
Primary referenceA structural view of the antibiotic degradation enzyme NDM-1 from a superbug., Guo Y, Wang J, Niu G, Shui W, Sun Y, Zhou H, Zhang Y, Yang C, Lou Z, Rao Z, Protein Cell. 2011 May;2(5):384-94. Epub 2011 Jun 2. PMID:21637961
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (3s0z.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (3s0z.pdb2.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 3S0Z
  • CSU: Contacts of Structural Units for 3S0Z
  • Structure Factors (185 Kb)
  • Retrieve 3S0Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3S0Z from S2C, [Save to disk]
  • Re-refined 3s0z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3S0Z 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 3S0Z
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3S0Z, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3s0z_A] [3s0z_B] [3s0z]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3S0Z: [Lactamase_B ] by SMART
    • Other resources with information on 3S0Z
  • Community annotation for 3S0Z at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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