7PFN | pdb_00007pfn

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Imipenem

• PDB DOI: https://doi.org/10.2210/pdb7PFN/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-11 Released: 2022-08-24 
• Deposition Author(s): Zhou, Q., He, Y., Jin, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.190 (DCC) 

Starting Model: experimental

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 

• DOI: https://doi.org/10.1021/acscentsci.3c00609

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.57 kDa 
• Atom Count: 4,435 
• Modelled Residue Count: 485 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth AAA], B [auth BBB]	260	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaOXA EC: 3.5.2.6
UniProt
Find proteins for A0A482LRD5 (Klebsiella pneumoniae) Explore A0A482LRD5  Go to UniProtKB:  A0A482LRD5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ID1 (Subject of Investigation/LOI)	C [auth AAA], H [auth BBB]	Imipenem C12 H19 N3 O4 S NIJGFQHESQFJAG-ZYUZMQFOSA-N
PO4	G [auth AAA]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
1BO	D [auth AAA], E [auth AAA], F [auth AAA], I [auth BBB], J [auth BBB]	1-BUTANOL C4 H10 O LRHPLDYGYMQRHN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.190 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.799	α = 90
b = 104.995	β = 90
c = 124.745	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Zhou, Q., He, Y., Jin, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31400663

Revision History  

• Version 1.0: 2022-08-24
  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: 2024-10-23
  Changes: Structure summary