7PFN

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Imipenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 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
Find similar proteins by:  (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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ID1 (Subject of Investigation/LOI)
Query on ID1

Download Ideal Coordinates CCD File 
C [auth AAA],
H [auth BBB]
Imipenem
C12 H19 N3 O4 S
NIJGFQHESQFJAG-ZYUZMQFOSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth AAA]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
1BO
Query on 1BO

Download Ideal Coordinates CCD File 
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
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: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.799α = 90
b = 104.995β = 90
c = 124.745γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2022-08-24
    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