2ZQ9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase Toho-1262Escherichia coliMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47066
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLS
Query on CLS

Download Ideal Coordinates CCD File 
E [auth A]CEPHALOTHIN
C16 H16 N2 O6 S2
XIURVHNZVLADCM-IUODEOHRSA-N
CEO
Query on CEO

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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
SPA
Query on SPA

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F [auth A]THIOPHENEACETIC ACID
C6 H6 O2 S
SMJRBWINMFUUDS-UHFFFAOYSA-N
SO4
Query on SO4

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B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.133 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.421α = 90
b = 72.421β = 90
c = 97.518γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary