7NRJ

Crystal Structure of a Class D carbapenemase complexed with iodide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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: 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
IOD (Subject of Investigation/LOI)
Query on IOD

Download Ideal Coordinates CCD File 
CA [auth DDD]
DA [auth DDD]
EA [auth DDD]
F [auth AAA]
G [auth AAA]
CA [auth DDD],
DA [auth DDD],
EA [auth DDD],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
O [auth BBB],
P [auth BBB],
Q [auth BBB],
R [auth BBB],
S [auth BBB],
W [auth CCC],
X [auth CCC],
Y [auth CCC]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
BA [auth DDD]
E [auth AAA]
K [auth BBB]
N [auth BBB]
T [auth CCC]
BA [auth DDD],
E [auth AAA],
K [auth BBB],
N [auth BBB],
T [auth CCC],
U [auth CCC],
Z [auth DDD]
1-BUTANOL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.764α = 90
b = 126.86β = 98.354
c = 111.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2022-03-23
    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