5N0I

Crystal structure of NDM-1 in complex with beta-mercaptoethanol - new refinement


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.110 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

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

  • 4EXY - determined by Strynadka, N.C.J., King, D.T.  

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, B
244Klebsiella 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
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.110 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.220α = 90.00
b = 107.220β = 90.00
c = 92.850γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references