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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.377 (Depositor), 0.378 (DCC)
R-Value Work:
0.307 (Depositor), 0.307 (DCC)
R-Value Observed:
0.315 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AUZ (Subject of Investigation/LOI) Query on A1AUZ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.377 (Depositor), 0.378 (DCC)
R-Value Work: 0.307 (Depositor), 0.307 (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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

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: 2024-06-19
Type: Initial release

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.