7PSE

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Oxacillin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.235 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history. 


Literature

An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity

Zhou, Q., Catalan, P., Bell, H., Baumann, P., Cooke, R., Evans, R., Yang, J., Zhang, Z., Zappala, D., Zhang, Y., Blackburn, G.M., He, Y., Jin, Y.

(2023) ACS Cent Sci 


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth AAA],
B [auth BBB]		260Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaOXA
EC: 3.5.2.6
UniProt
Find proteins for A0A482LRD5 (Klebsiella pneumoniae)
Explore A0A482LRD5 
Go to UniProtKB:  A0A482LRD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482LRD5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1S6 (Subject of Investigation/LOI)
Query on 1S6
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C [auth AAA],
G [auth BBB]		(2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid
C19 H21 N3 O5 S
QXXMSXCGXIRLPM-ISTRZQFTSA-N
1BO
Query on 1BO
Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA],
H [auth BBB],
I [auth BBB]		1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
F [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY		A [auth AAA],
B [auth BBB]		L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.235 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.83α = 90
b = 105.48β = 90
c = 124.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SADABSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31400663

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Refinement description
  • Version 2.1: 2024-01-31
    Changes: Refinement description
  • Version 2.2: 2024-03-06
    Changes: Database references
  • Version 2.3: 2024-10-16
    Changes: Structure summary