9C83 | pdb_00009c83

X-ray crystal structure of AmpC beta-lactamase with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9C83/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-11 Released: 2024-06-19 
• Deposition Author(s): Liu, F., Shoichet, B.K.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.377 (Depositor), 0.380 (DCC) 
• R-Value Work: 
  0.307 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.315 (Depositor) 

Starting Model: experimental

Literature

Improved correlations with score, hit-rate, and affinity as docking library and testing scale increase

Liu, F., Shoichet, B.K., Bassim, V.

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.

Macromolecule Content 

• Total Structure Weight: 83.93 kDa 
• Atom Count: 5,531 
• Modeled Residue Count: 712 
• Deposited Residue Count: 754 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AmpC Beta-lactamase	A, B	377	Escherichia coli	Mutation(s): 0  Gene Names: ampC, ampA, b4150, JW4111 EC: 3.5.2.6
UniProt
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AUZ (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-[(3M)-3-(5-chloro-1,2,3-thiadiazol-4-yl)phenyl]-5-methyl-3-oxo-2,3-dihydro-1,2-oxazole-4-sulfonamide C12 H9 Cl N4 O4 S2 DQBOCBWXJZVOII-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.377 (Depositor), 0.380 (DCC) 
• R-Value Work:  0.307 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.315 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.774	α = 90
b = 77.03	β = 115.47
c = 100.079	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Liu, F., Shoichet, B.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release