5ZJ8

Crystal structure of NDM-1 in complex with D-captopril derivative CY32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of NDM-1

Zhang, H.Hao, Q.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A
242Klebsiella 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
9DC
Query on 9DC

Download SDF File 
Download CCD File 
A
(2S)-2,3-disulfanylpropan-1-ol
C3 H8 O S2
WQABCVAJNWAXTE-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.118 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.491α = 90.00
b = 59.949β = 98.11
c = 41.946γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-19 
  • Released Date: 2019-03-20 
  • Deposition Author(s): Zhang, H., Hao, Q.

Funding OrganizationLocationGrant Number
National Science Foundation (China)China31670753

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release