5NBK

NDM-1 metallo-beta-lactamase: a parsimonious interpretation of the diffraction data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5A5Z - determined by Klingler, F.M., Wichelhaus, T.A., Frank, D., Cuesta-Bernal, J., El-Delik, J., Mueller, H.F., Sjuts, H., Goettig, S., Koenigs, A., Pogoryelov, D., Proschak, E.  

Literature

A close look onto structural models and primary ligands of metallo-beta-lactamases.

Raczynska, J.E.Shabalin, I.G.Minor, W.Wlodawer, A.Jaskolski, M.

(2018) Drug Resist. Updat. 40: 1-12


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A, C
251Klebsiella 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, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 108.047α = 90.00
b = 108.047β = 90.00
c = 92.571γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Research and DevelopmentPolandAMR/1/2015

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references
  • Version 1.2: 2019-03-13
    Type: Data collection, Experimental preparation