7O5N

Crystal Structure of a Class D carbapenemase complexed with Avibactam


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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],
C [auth CCC],
D [auth DDD]
260Klebsiella pneumoniaeMutation(s): 0 
Gene Names: bla OXA-48bla_2blaOXA-48G5637_27540KPE71T_00045SAMEA3649466_05396
EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL (Subject of Investigation/LOI)
Query on NXL

Download Ideal Coordinates CCD File 
G [auth AAA],
N [auth BBB],
R [auth CCC],
W [auth DDD]
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth BBB],
P [auth CCC],
V [auth DDD]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
1BO
Query on 1BO

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E [auth AAA],
F [auth AAA],
L [auth BBB],
M [auth BBB],
Q [auth CCC]
1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
H [auth AAA]
I [auth AAA]
J [auth AAA]
O [auth BBB]
S [auth CCC]
H [auth AAA],
I [auth AAA],
J [auth AAA],
O [auth BBB],
S [auth CCC],
T [auth CCC],
U [auth CCC],
X [auth DDD]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.749α = 90
b = 107.959β = 90
c = 125.675γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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: 2022-04-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Database references