4U4L

Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the metallo-beta-lactamase NDM-1 in complex with a bisthiazolidine inhibitor

Kosmopoulou, M.Hinchliffe, P.Spencer, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase NDM-1
A, B, C, D
246Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3C7
Query on 3C7

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
R [auth D]
(3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid
C7 H11 N O2 S3
ZTWVMVSSSBGFHH-JKUQZMGJSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth C],
Q [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
O [auth D],
P [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.57α = 87.39
b = 69.023β = 88.21
c = 69.646γ = 76.75
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesAI100560

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description