6EWE

Crystal structure of BCII Metallo-beta-lactamase in complex with DZ-308


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases.

Zhang, D.Markoulides, M.S.Stepanovs, D.Rydzik, A.M.El-Hussein, A.Bon, C.Kamps, J.J.A.G.Umland, K.D.Collins, P.M.Cahill, S.T.Wang, D.Y.von Delft, F.Brem, J.McDonough, M.A.Schofield, C.J.

(2018) Bioorg. Med. Chem. 26: 2928-2936


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A
227Bacillus cereusMutation(s): 0 
Gene Names: blm
EC: 3.5.2.6
Find proteins for P04190 (Bacillus cereus)
Go to UniProtKB:  P04190
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
C0W
Query on C0W

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Download CCD File 
A
(~{Z})-3-(1-benzothiophen-3-yl)-2-sulfanyl-prop-2-enoic acid
C11 H8 O2 S2
RAMCKYVBVNEIFT-UITAMQMPSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.139 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 53.190α = 90.00
b = 61.010β = 92.99
c = 69.540γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--
Wellcome TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release