6D1G

Crystal structure of NDM-1 complexed with compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A conserved substrate envelope in serine and metallo-carbapenemases enables cross-class inhibitor discovery

Pemberton, O.A.Jaishankar, P.Renslo, A.R.Chen, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metallo-beta-lactamase type 2
A
233Klebsiella 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
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
YKG
Query on YKG

Download SDF File 
Download CCD File 
A
[(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
C11 H10 Br O5 P
AVDUOTYJUPESMO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.134 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.500α = 90.00
b = 60.150β = 98.10
c = 41.850γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01AI103158-04

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release