4RBS

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of New Delhi Metallo-beta-Lactamase-1 in the Complex with Hydrolyzed Meropenem

Kim, Y.Tesar, C.Jedrzejczak, R.Babnigg, G.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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
0RV
Query on 0RV

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Download CCD File 
A, B
(2S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-3-methyl-2H-pyrrole-5-carboxylic acid
Meropenem, hydroxylated form
C17 H25 N3 O6 S
AGLQJULLKPLWOW-YBXAARCKSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.405 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.428α = 90.00
b = 74.428β = 90.00
c = 219.960γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SBC-Collectdata collection
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-11-26
    Type: Initial release