3NCK | pdb_00003nck

Crystal Structure of BlaC-E166A covalently bound with Nafcillin

• PDB DOI: https://doi.org/10.2210/pdb3NCK/pdb

• Classification: Hydrolase/Antibiotic
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-06-04 Released: 2011-12-14 
• Deposition Author(s): Tremblay, L.W., Blanchard, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

BlaC-E166A covalently bound with cephalosporins and penicillins

Tremblay, L.W., Blanchard, J.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.63 kDa 
• Atom Count: 1,983 
• Modeled Residue Count: 256 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	265	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: blaA, blaC, MT2128, MTCY49.07c, Rv2068c EC: 3.5.2.6
UniProt
Find proteins for P9WKD3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKD3  Go to UniProtKB:  P9WKD3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NFF	B [auth A]	(2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C21 H24 N2 O5 S XDLYHUOUOKHAMD-DKSSEZFCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.671	α = 90
b = 67.822	β = 90
c = 76.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-14 
Deposition Author(s): Tremblay, L.W., Blanchard, J.S.

Revision History  

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Other
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-06-20
  Changes: Data collection, Structure summary
• Version 1.4: 2018-10-03
  Changes: Data collection
• Version 1.5: 2019-04-03
  Changes: Data collection, Derived calculations
• Version 1.6: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.7: 2024-10-16
  Changes: Structure summary