2P9V | pdb_00002p9v

Structure of AmpC beta-lactamase with cross-linked active site after exposure to small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb2P9V/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-03-26 Released: 2007-08-14
Deposition Author(s): Babaoglu, K., Wyrembak, P.N., Pelto, R.B., Shoichet, B.K., Pratt, R.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.197 (Depositor), 0.196 (DCC)
R-Value Work:
0.160 (Depositor), 0.160 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

O-Aryloxycarbonyl Hydroxamates: New beta-Lactamase Inhibitors That Cross-Link the Active Site.

Wyrembak, P.N., Babaoglu, K., Pelto, R.B., Shoichet, B.K., Pratt, R.F.

(2007) J Am Chem Soc 129: 9548-9549

PubMed: 17628063 Search on PubMed
DOI: https://doi.org/10.1021/ja072370u
Primary Citation Related Structures:
2P9V

Organizational Affiliation

Department of Chemistry, Wesleyan University, Middletown, Connecticut 06459, USA.

Macromolecule Content

Total Structure Weight: 79.31 kDa
Atom Count: 6,711
Modeled Residue Count: 713
Deposited Residue Count: 716
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	358	Escherichia coli	Mutation(s): 1 Gene Names: ampC, ampA 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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	B	358	Escherichia coli	Mutation(s): 0 Gene Names: ampC, ampA 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
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.197 (Depositor), 0.196 (DCC)
R-Value Work: 0.160 (Depositor), 0.160 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.02	α = 90
b = 76.434	β = 116.07
c = 97.786	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary