4U4L | pdb_00004u4l

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

• PDB DOI: https://doi.org/10.2210/pdb4U4L/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-23 Released: 2014-08-20 
• Deposition Author(s): Kosmopoulou, M., Hinchliffe, P., Spencer, J.
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 105.71 kDa 
• Atom Count: 7,459 
• Modeled Residue Count: 907 
• Deposited Residue Count: 984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase NDM-1	A, B, C, D	246	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3C7	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	M [auth C], Q [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	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

Binding Affinity Annotations
ID	Source	Binding Affinity
3C7	BindingDB:  4U4L	Ki: 7000 (nM) from 1 assay(s)
		IC50: 1.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.57	α = 87.39
b = 69.023	β = 88.21
c = 69.646	γ = 76.75

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Kosmopoulou, M., Hinchliffe, P., Spencer, J.

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	AI100560

Revision History  

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