6WHF

class C beta-lactamase from Escherichia coli in complex with cephalothin

PDB DOI: https://doi.org/10.2210/pdb6WHF/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Escherichia coli A35218R
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-04-08 Released: 2020-04-22
Deposition Author(s): Chang, C., Maltseva, N., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

class C beta-lactamase from Escherichia coli in complex with Cephalothin

Chang, C., Maltseva, N., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 80.67 kDa
Atom Count: 6,254
Modelled Residue Count: 718
Deposited Residue Count: 718
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	359	Escherichia coli A35218R	Mutation(s): 0 Gene Names: bla(ampc-EC31), blaEC, AJ318_17250, AZZ83_002790, D7Y10_20755, D7Y10_27165, D9L99_20655, D9L99_27090, DJ487_18405, DW236_18485... bla(ampc-EC31), blaEC, AJ318_17250, AZZ83_002790, D7Y10_20755, D7Y10_27165, D9L99_20655, D9L99_27090, DJ487_18405, DW236_18485, ELT23_15185 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9EP (Subject of Investigation/LOI) Query on 9EP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	H [auth A], M [auth B]	(2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C₁₆ H₁₈ N₂ O₆ S₂ MXSQWXIVWHYOCY-IUODEOHRSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Interactions & Density Focus chain H [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.181
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/m36whf

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.185	α = 90
b = 46.298	β = 116.58
c = 108.854	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-04-22

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2020-04-22
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary