9DHL

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

• PDB DOI: https://doi.org/10.2210/pdb9DHL/pdb
• Entry: 9DHL supersedes: 9C8J

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


• Deposited: 2024-09-04 Released: 2024-10-23 
• 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: 1.88 Å
• R-Value Free: 0.180 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Starting Model: experimental

Literature

The impact of Library Size and Scale of Testing on Virtual Screening

Liu, F., Shoichet, B.K.

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: 83.92 kDa 
• Atom Count: 6,369 
• Modelled Residue Count: 716 
• 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
A1AU5 (Subject of Investigation/LOI)	C [auth A], D [auth B]	N-(1-acetyl-2,3-dihydro-1H-indol-4-yl)-3-chloro-2-hydroxybenzene-1-sulfonamide C16 H15 Cl N2 O4 S OIXKKLRRYRMQMK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.180 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.28	α = 90
b = 76.93	β = 116.545
c = 97.72	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: 2024-10-23 
Deposition Author(s): Liu, F., Shoichet, B.K.
• This entry supersedes: 9C8J

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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: 2024-10-23
  Type: Initial release