7PEP

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 

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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HIW (Subject of Investigation/LOI)
Query on HIW

Download Ideal Coordinates CCD File 
E [auth AAA],
G [auth BBB],
M [auth CCC],
O [auth DDD]
(2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid
C12 H19 N3 O5 S
GGEWNUMDSNUHAH-LURQLKTLSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
F [auth AAA]
H [auth BBB]
I [auth BBB]
J [auth BBB]
N [auth CCC]
F [auth AAA],
H [auth BBB],
I [auth BBB],
J [auth BBB],
N [auth CCC],
P [auth DDD]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
1BO
Query on 1BO

Download Ideal Coordinates CCD File 
K [auth CCC],
L [auth CCC]
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: 1.70 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.946α = 90
b = 107.93β = 90
c = 124.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata 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: 2022-08-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Database references