7O5Q

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Oxacillin

Zhou, Q.He, Y.Jin, Y.

To be published.

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)
Go to UniProtKB:  Q6XEC0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V3H (Subject of Investigation/LOI)
Query on V3H

Download Ideal Coordinates CCD File 
S [auth CCC],
Z [auth DDD]
(2R,4S)-2-[(1R)-2-butoxy-1-[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonylamino]-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidin-3-ium-4-carboxylic acid
C23 H30 N3 O6 S
KTVAJMKGNMTGBA-CMKODMSKSA-O
0WO (Subject of Investigation/LOI)
Query on 0WO

Download Ideal Coordinates CCD File 
Q [auth CCC],
X [auth DDD]
(2R,4S)-2-[(R)-carboxy{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carbo xylic acid
C19 H21 N3 O6 S
JCHZLBSPYSDECZ-OFQRWUPVSA-N
IOD (Subject of Investigation/LOI)
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth DDD]
BA [auth DDD]
F [auth AAA]
G [auth AAA]
H [auth AAA]
AA [auth DDD],
BA [auth DDD],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
L [auth BBB],
M [auth BBB],
N [auth BBB],
O [auth BBB],
P [auth BBB],
T [auth CCC],
U [auth CCC],
V [auth CCC],
W [auth CCC]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth AAA],
J [auth BBB],
R [auth CCC]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
1BO
Query on 1BO

Download Ideal Coordinates CCD File 
K [auth BBB],
Y [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: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.053α = 90
b = 126.902β = 98.289
c = 111.201γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata 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: 2022-04-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description