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)

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
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

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

Liu, F., Shoichet, B.K.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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)) Go to UniProtKB: P00811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AU5 (Subject of Investigation/LOI) Query on A1AU5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B]

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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

This entry supersedes: 9C8J

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

Revision History (Full details and data files)

Version 1.0: 2024-10-23
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.