5ZJC

Crystal structure of NDM-1 in complex with D-captopril derivative CY41


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation 3D Report Full Report



Literature

Crystal structure of NDM-1

Zhang, H.Hao, Q.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2A242Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9EX
Query on 9EX

Download CCD File 
A
(2S)-2-methyl-3-sulfanyl-propan-1-ol
C4 H10 O S
FCIVYWQHILCTLI-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.96 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.61α = 90
b = 59.98β = 97.88
c = 42.067γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-20 
  • 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