Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.60 kDa 
• Atom Count: 2285 
• Modelled Residue Count: 265 
• Deposited Residue Count: 265 
• Unique protein chains: 1

1VM1

STRUCTURE OF SHV-1 BETA-LACTAMASE INHIBITED BY TAZOBACTAM

• PDB DOI: 10.2210/pdb1VM1/pdb
• Entry: 1VM1 supersedes: 1G56

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli str. K-12 substr. DH10B
• Mutation(s): No 


• Deposited: 2004-08-27 Released: 2004-09-07 
• Deposition Author(s): Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A., Bonomo, R.A., Knox, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.257 
• R-Value Work: 0.171 
• R-Value Observed: 0.177 

Literature

Inhibition of the SHV-1 beta-lactamase by sulfones: crystallographic observation of two reaction intermediates with tazobactam.

Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A., Bonomo, R.A., Knox, J.R.

(2001) Biochemistry 40: 1861-1866

• PubMed: 11327849 
• DOI: 10.1021/bi0022745
• Primary Citation of Related Structures:  
  1VM1


• PubMed Abstract: 
  

Two species resulting from the reaction of the SHV-1 class A beta-lactamase with the sulfone inhibitor tazobactam have been trapped at 100 K and mapped by X-ray crystallography at 2.0 A resolution. An acyclic form of tazobactam is covalently bonded to the catalytic Ser70 side chain, and a second species, a five-atom vinyl carboxylic acid fragment of tazobactam, is bonded to Ser130. It is proposed that the electron density map of the crystal is a composite picture of two complexes, each with only a single bound species. It is estimated that the two complexes exist in the crystal in approximately equal populations. Results are discussed in relation to the mechanism-based inhibition of class A beta-lactamases by the similar inhibitors sulbactam and clavulanic acid.

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Related Citations: 

• Structure of the SHV-1 Beta-Lactamase
  Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A.M., Bonomo, R.A., Knox, J.R.
  (1999) Biochemistry 38: 5720

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Organizational Affiliation: 

Department of Molecular and Cell Biology, The University of Connecticut, Storrs, CT 06269-3125, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE SHV-1	A	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, shv1 EC: 3.5.2.6
UniProt
Find proteins for P0AD64 (Klebsiella pneumoniae) Explore P0AD64  Go to UniProtKB:  P0AD64

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MA4	B [auth A], F [auth A]	CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE C24 H44 O11 WUCWJXGMSXTDAV-QKMCSOCLSA-N
TBE	C [auth A]	TAZOBACTAM INTERMEDIATE C10 H14 N4 O5 S ANZZKUOZZHRUQC-AARLMMRRSA-N
TAZ	E [auth A]	TAZOBACTAM C10 H12 N4 O5 S LPQZKKCYTLCDGQ-NRPADANISA-N
AKR	D [auth A]	ACRYLIC ACID C3 H4 O2 NIXOWILDQLNWCW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TAZ	BindingDB:  1VM1	Ki: 220 (nM) from 1 assay(s)
		IC50: min: 30, max: 222 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.257 
• R-Value Work: 0.171 
• R-Value Observed: 0.177 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.2	α = 90
b = 56.1	β = 90
c = 82.5	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-27 
• Released Date: 2004-09-07 
Deposition Author(s): Kuzin, A.P., Nukaga, M., Nukaga, Y., Hujer, A., Bonomo, R.A., Knox, J.R.
• This entry supersedes: 1G56

Revision History  

• Version 1.0: 2004-09-07
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description