2ZQ9 | pdb_00002zq9

Cephalothin acyl-intermediate structure of class a beta-lactamase Toho-1 E166A/R274N/R276N triple mutant

PDB DOI: https://doi.org/10.2210/pdb2ZQ9/pdb

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

Deposited: 2008-08-07 Released: 2009-07-28
Deposition Author(s): Nitanai, Y., Shimamura, T., Uchiyama, T., Ishii, Y., Takehira, M., Yutani, K., Matsuzawa, H., Miyano, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 ?
R-Value Free:
0.146 (Depositor), 0.140 (DCC)
R-Value Work:
0.133 (Depositor), 0.130 (DCC)
R-Value Observed:
0.133 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis of Extend Spectrum Beta-Lactamase in Correlation of Enzymatic Kinetics and Thermal Stability of Acyl-Intermediates

Nitanai, Y., Shimamura, T., Uchiyama, T., Ishii, Y., Takehira, M., Yutani, K., Matsuzawa, H., Miyano, M.

To be published.

Macromolecule Content

Total Structure Weight: 29.19 kDa
Atom Count: 2,549
Modelled Residue Count: 259
Deposited Residue Count: 262
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 Toho-1	A	262	Escherichia coli	Mutation(s): 3 Gene Names: bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066 Go to UniProtKB: Q47066
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47066
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLS Query on CLS Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CEPHALOTHIN C₁₆ H₁₆ N₂ O₆ S₂ XIURVHNZVLADCM-IUODEOHRSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CEO Query on CEO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	5-METHYLENE-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-5,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID C₁₄ H₁₄ N₂ O₄ S₂ FYGLCWWPHIWVKN-ZWNOBZJWSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SPA Query on SPA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	THIOPHENEACETIC ACID C₆ H₆ O₂ S SMJRBWINMFUUDS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]