4HKY

New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.004 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Faropenem

Kim, Y.Tesar, C.Jedrzejczak, R.Babnigg, J.Mire, J.Sacchettini, J.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase NDM-1
A, B
243Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Go to UniProtKB:  C7C422
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SFR
Query on SFR

Download SDF File 
Download CCD File 
A, B
(2R)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-5-[(2R)-oxolan-2-yl]-2,3-dihydro-1,3-thiazole-4-carboxylic acid
FAROPENEM, unbound, hydrolyzed form
C12 H17 N O6 S
CGJDLFMMMJEANA-DAGMQNCNSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FPM
Query on FPM

Download SDF File 
Download CCD File 
A, B
(5R,6S)-6-(1-hydroxyethyl)-7-oxo-3-[(2R)-oxolan-2-yl]-4-thia-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid
Faropenem
C12 H15 N O5 S
HGGAKXAHAYOLDJ-FHZUQPTBSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 145.627α = 90.00
b = 39.324β = 99.96
c = 75.370γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000phasing
PHENIXrefinement
SBC-Collectdata collection
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Non-polymer description