3Q07 | pdb_00003q07

CTX-M-9 S70G in complex with piperacillin

PDB DOI: https://doi.org/10.2210/pdb3Q07/pdb

Classification: Hydrolase/Antibiotic
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-12-15 Released: 2011-12-21
Deposition Author(s): Delmas, J., Leyssne, D., Robin, F., Coignoux, A., Bonnet, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.175 (Depositor), 0.175 (DCC)
R-Value Work:
0.146 (Depositor), 0.145 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CTX-M-9 S70G mutant in complex with piperacillin

Leyssne, D., Delmas, J., Coignoux, A., Robin, F., Bonnet, R.

To be published.

Macromolecule Content

Total Structure Weight: 58.53 kDa
Atom Count: 5,031
Modeled Residue Count: 522
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	263	Escherichia coli	Mutation(s): 1 Gene Names: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9b EC: 3.5.2.6
UniProt
Find proteins for Q9L5C8 (Escherichia coli) Explore Q9L5C8 Go to UniProtKB: Q9L5C8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9L5C8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YPP Query on YPP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	Hydrolyzed piperacillin C₂₃ H₂₉ N₅ O₈ S OKSUEATVFIVTFV-WBTNSWJXSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]
WPP Query on WPP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	Piperacillin C₂₃ H₂₇ N₅ O₇ S IVBHGBMCVLDMKU-GXNBUGAJSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.175 (Depositor), 0.175 (DCC)
R-Value Work: 0.146 (Depositor), 0.145 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.128	α = 90
b = 106.34	β = 101.9
c = 47.61	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-21
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

3Q07 | pdb_00003q07

CTX-M-9 S70G in complex with piperacillin

Literature

CTX-M-9 S70G mutant in complex with piperacillin

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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